Systems and methods for automated cell culture

Abstract

To provide a cell culture system and method which improve efficiency, and restrict potential contamination during cell culture.SOLUTION: In some embodiments, one or a plurality of cell culture devices are fluid-connected to one or a plurality of multi-port valves 2007 and one or a plurality of fluid pumps. The fluid pump can be pumped so as to take in or out various kinds of fluid to / from the cell culture devices as required in order to assist with the growth of cells routed by one or a plurality of multi-port valves. In some embodiments, one or a plurality of constituents are removable from other constituents, and as a result, some constituents can be independently prepared and sterilized before use.SELECTED DRAWING: Figure 35

Description

[Technical Field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims the benefit of priority to U.S. Provisional Application No. 62 / 719,652, entitled "Automated Cell Culture," filed August 19, 2018, which is incorporated herein by reference in its entirety.

[0002] FIELD OF THE INVENTION The present disclosure relates generally to systems and methods for culturing cells. [Background technology]

[0003] Cells can be grown or cultured under controlled conditions in laboratory or industrial environments for a variety of purposes. Typically, cells are grown inside a sealed vessel and covered with a solution called cell culture medium, which provides essential nutrients and other supplements to promote cell growth. Examples of vessels used in cell culture include flat, circular dishes such as Petri dishes and laboratory flasks. As cells grow and proliferate, they consume nutrients from the cell culture medium and produce waste by-products. For this reason, the cell culture medium must be periodically replaced so that the cells continue to multiply. Additionally, cell cultures can be expanded by transferring a portion of the cells to a new vessel, providing additional volume or area in which the cells can grow. This process of transferring a portion of the cells to a new vessel is sometimes called passaging or subculturing. Additionally, cells can be removed from the vessel in preparation for their use. The process of separating the cells from the vessel in which they are grown is sometimes called harvesting.

[0004] Cultures of cells typically grow according to a standard growth pattern. The first stage of growth after a culture is seeded is a lag phase, a period of slow growth as the cells adapt to the culture environment. The lag phase is followed by a logarithmic phase, during which the cells grow exponentially and consume nutrients in the growth medium. When a culture of cells consumes all nutrients in the growth medium or reaches the capacity of the environment by occupying all available space, growth slows and the cells enter a stationary or plateau phase, during which growth is significantly reduced or completely halted. Known cell culture treatments often include passaging the cells before they enter this stationary phase to optimize growth.

[0005] Adherent cells grow by attaching to a surface, such as the bottom of a culture flask or dish. The amount of cells in a flask is usually measured as the percentage of the growth surface covered by cells, called the percentage confluence. Adherent cells must be detached from the surface before they can be removed from the vessel. Cells can be detached by one of several methods, including mechanical scraping or using enzymes such as trypsin to break their adhesion to the vessel surface. The detached cells are then resuspended in fresh growth medium and returned to the growth surface to allow them to settle.

[0006] These processes—removing spent medium from a cell culture vessel, adding fresh medium, detaching adherent cells, and transferring cells from one vessel to another—are typically performed by laborious manual procedures. For example, known cell culture methods frequently involve repetitive operations, including moving cells (within the cell culture vessel) between various work stations and / or opening the cell culture vessel and transferring fluids in and out of the vessel. Specifically, known methods involve first loading cells and cell culture medium into a vessel in a sterile environment (e.g., a laminar flow hood). When ready, the cell culture vessel is closed (to minimize contamination) and moved to an incubator to promote growth. Cell culture vessels are often manually monitored to determine the appropriate time to change the cell culture medium, and are periodically manually monitored to inspect parameters such as confluence and cell morphology by removing the vessel from the incubator and imaging it under a microscope. These manual monitoring steps typically require travel to a lab to check the culture and determine whether any additional operations need to be performed. When it is time to change the cell culture medium, the cell culture vessel is then moved from the incubator to a sterile environment, opened (or connected to a source of waste and fresh cell culture medium), and fluids are transferred to and / or from the cell culture vessel. The vessel may also be moved and / or opened to complete other operations, such as cell passaging or cell harvesting.

[0007] Such known procedures are inefficient, costly, and prone to contamination. For example, repeatedly opening the cell culture system and moving the cell incubator between experimental stations can expose cells to contamination. Furthermore, all manually performed operations are costly and susceptible to contamination (or cell damage) if the operator does not follow the proper procedures. Furthermore, determining when to change the medium or when to passage the cells is usually done according to a predetermined schedule, which may not be optimal. Adhering to a set schedule can result in additional (and potentially unnecessary) use of a laminar flow hood (which can be costly because its operation can consume a large amount of energy). Adhering to a set schedule can also result in reduced efficiency of cell growth (e.g., if cell growth reaches a plateau phase before the cell culture medium is changed).

[0008] Therefore, a need exists for a cell culture system that improves efficiency and limits potential contamination during cell culture. Specifically, a need exists for systems and methods that automate cell culture procedures, maintain the cell culture system in a closed, sterile environment during culture, and allow for efficient setup and use. A need also exists for an automated cell culture system that can optionally operate with existing, off-the-shelf cell culture equipment. Summary of the Invention

[0009] According to certain implementations, the present specification describes systems and methods for automatically culturing cells. The automated cell culture systems disclosed herein enable scientists to accelerate their research and development by automating manual cell culture. In various embodiments, the disclosed systems and methods may provide automated cell growth medium replenishment, automated cell passaging, and / or automated cell culture analysis. These automated cell culture systems and methods can increase efficiency and reduce errors compared to manual cell culture operations. Furthermore, these embodiments increase the quantity and quality of cell culture-related data points available to scientists through integrated automated analysis mechanisms.

[0010] An automated cell culture system according to embodiments includes a housing having a valve actuator and a fluid pump disposed therein. The automated cell culture system also includes a removable tray configured to removably mate with the housing. A plurality of cell culture vessel brackets attached to the removable tray are configured to hold respective ones of the plurality of cell culture vessels, each cell culture vessel being covered with a sterile lid. A selector valve is configured to couple to the valve actuator of the housing when the removable tray is mated with the housing. In some embodiments, a plurality of media sources external to the housing and the removable tray can be provided. A multiport selector valve is configured to fluidly connect a master port to selected ports of a plurality of selectable ports, the master port of the multiport selector valve being fluidly connected to the fluid pump, and each of the plurality of cell culture vessels and the media source being fluidly connected directly to a respective one of the plurality of selectable ports of the multiport selector valve. In some embodiments, the plurality of cell culture vessels and their sterile lids, the multiport selector valve, and the fluid connections therebetween form a first sterile sealed system attached to the removable tray.

[0011] In some embodiments, a method of cell line maintenance using an automated cell culture system includes sending a command to a mobile imaging system of the automated cell culture system to image cells in a selected vessel of the automated cell culture system, receiving an image of the cells in the selected vessel from the imaging system, determining a cell passaging criterion based on the image of the cells in the selected vessel, comparing the cell passaging criterion to a threshold cell passaging criterion, and determining, based on the comparison, to initiate passaging of the cells in the selected vessel to a subculture vessel. The method of cell line maintenance also includes passaging a configured portion of the cells in the selected vessel to a subculture vessel, and sending a notification that the automated cell culture system has passaged the configured portion of the cells in the selected vessel to the subculture vessel. Other embodiments of this aspect include corresponding computer systems, devices, and computer programs recorded on one or more computer storage devices, each configured to perform the operations of the method.

[0012] The details of one or more implementations of the subject matter described herein are set forth in the accompanying drawings and the description below. Other potential features, aspects, and advantages of the subject matter will become apparent from the description, drawings, and claims.

[0013] The present disclosure will become more fully understood from the detailed description and the accompanying drawings, wherein: [Brief explanation of the drawings]

[0014] [Figure 1A] 1 shows a schematic diagram of an automated cell culture system according to an embodiment. [Figure 1B] 1 shows a schematic diagram of an automated cell culture system according to an embodiment. [Figure 2] 1 shows a top view of an automated cell culture system according to an embodiment. [Figure 3A] 1 shows a top view of a base housing of an automated cell culture system according to an embodiment. [Figure 3B] 1 illustrates a removable tray assembly of an automated cell culture system according to an embodiment. [Figure 4] 1 illustrates an exemplary removable tray of an automated cell culture system mated to an exemplary base housing, according to an embodiment. [Figure 5] 1 illustrates a cross-sectional view of an exemplary multi-port valve according to an embodiment. [Figure 6A] 1 illustrates an exemplary multi-port valve according to an embodiment. [Figure 6B] 1 illustrates a bottom view of an exemplary multi-port valve. [Figure 7] 1 illustrates a lid for a cell culture vessel according to an embodiment. [Figure 8] 1 shows a cross-sectional view of a lid of a cell incubator according to an embodiment. [Figure 9] 1 illustrates steps of a method for transferring a liquid from a first vessel to a second vessel using an automated cell culture system with a single-port pump, according to an embodiment. [Figure 10] 1 illustrates steps of a method for transferring a liquid from a first vessel to a second vessel using an automated cell culture system with a two-port pump according to an embodiment. [Figure 11] 1 shows steps of a method for changing cell culture medium during maintenance of adherent cell lines. [Figure 12] 1 illustrates steps of a method for the maintenance or propagation of adherent cell lines with passaging to new cell culture vessels. [Figure 13] 1 illustrates the steps of a method for maintenance of suspension cell lines with optional passaging. [Figure 14] 1 shows steps of a method for suspension cell line propagation. [Figure 15] 1 illustrates an exemplary machine of a computer system within which a set of instructions may be executed to cause the machine to perform any one or more of the methodologies discussed herein. [Figure 16A] FIG. 1 is a schematic diagram of a tray assembly of a cell culture system, according to an embodiment. [Figure 16B] FIG. 1 is a schematic diagram of a base unit of a cell culture system, according to an embodiment. [Figure 16C]16B is a schematic diagram of a cell culture system according to an embodiment, including a tray assembly as shown in FIG. 16A and a base unit as shown in FIG. 16B. [Figure 17] FIG. 1 is a schematic diagram of an electronic control system for a cell culture system, according to an embodiment. [Figure 18] 18-20 are each example screenshots showing various GUI elements generated in connection with the operation of the electronic control system. [Figure 19] 18-20 are each example screenshots showing various GUI elements generated in connection with the operation of the electronic control system. [Figure 20] 18-20 are each example screenshots showing various GUI elements generated in connection with the operation of the electronic control system. [Figure 21] FIG. 1 is a top view of a tray assembly of a cell culture system, according to an embodiment. [Figure 22] FIG. 22 is a top view of the tray assembly of FIG. 21 positioned within the protective overwrap. [Figure 23] FIG. 22 is a top view of the tray assembly of FIG. 21 showing a fluid pump coupled to the tray assembly. [Figure 24] 24 is a perspective view of the tray assembly of FIG. 21 showing the fluid pump of FIG. 23 coupled to the tray assembly. [Figure 25] 22 is a perspective view of the tray assembly of FIG. 21 showing cell culture vessels coupled to the tray assembly. [Figure 26] 24 is a top view of FIG. 21 showing three cell culture vessels coupled to the fluid pump and tray assembly of FIG. 23. [Figure 27] FIG. 22 is a top view of the tray assembly of FIG. 21, showing connection with a base unit, according to an embodiment. [Figure 28] FIG. 28 is a perspective view of a multiport valve coupled to the base unit of FIG. 27. [Figure 29] FIG. 28 is a top view of a portion of the base unit of FIG. 27. [Figure 30] 28 is a perspective view of the tray assembly of FIG. 21 coupled to the base unit of FIG. 27. [Figure 31] 1 is a flowchart illustrating a method of preparing a cell culture system for use in a cell culture procedure, according to an embodiment. [Figure 32] FIG. 1 is a perspective view of an imaging device of a base unit of a cell culture system, according to an embodiment. [Figure 33] FIG. 33 is a top view of the imaging device of FIG. 32. [Figure 34] FIG. 33 is a side view of the imaging device of FIG. 32. [Figure 35] FIG. 1 is a perspective view of a tray assembly of a cell culture system according to another embodiment. [Figure 36] FIG. 36 is a perspective view of a portion of the tray assembly of FIG. 35 with removable components removed. [Figure 37] 36 is a perspective view of a portion of the tray assembly of FIG. 35, showing the multiport valve, lid, and fluid pump coupled to the tray. [Figure 38] FIG. 36 is a perspective view of a base unit of a cell culture system that can be used with the tray assembly of FIG. 35. [Figure 39] FIG. 39 is a perspective view of the pump actuator of the base unit of FIG. 38. [Figure 40] FIG. 39 is a perspective view of the base unit of FIG. 38 with a fluid pump and a multiport valve connected thereto. [Figure 41] FIG. 39 is a partially exploded view of a portion of the base unit of FIG. 38 showing the multi-port valve before assembly to the base unit. [Figure 42] FIG. 39 is a side view of the base unit of FIG. 38. [Figure 43] FIG. 39 is a side view of the base unit of FIG. 38 showing the interior of the base unit. [Figure 44] 39A-39C are opposing side views of the base unit of FIG. 38 showing the interior of the base unit. [Figure 45] FIG. 1 is a perspective view of a cell culture system according to another embodiment. [Figure 46] FIG. 46 is a top view of the cell culture system of FIG. 45. [Figure 47] FIG. 47 is a cross-sectional view taken along line 47-47 in FIG. [Figure 48] FIG. 1 is a perspective view of a tray assembly, according to an embodiment. [Figure 49] FIG. 49 is a top view of the tray assembly of FIG. 48. [Figure 50] FIG. 50 is a cross-sectional view taken along line 50-50 of FIG. 49. [Figure 51] FIG. 1 is a perspective view of a base unit, according to an embodiment. [Figure 52] FIG. 1 is a diagram of a cell culture system according to another embodiment. [Figure 53] FIG. 53 is a side view of the cell culture system of FIG. 52 showing the imaging system positioned inside the base unit. [Figure 54] FIG. 53 is a top view of the base unit of the cell culture system of FIG. 52. [Figure 55] FIG. 53 is a top view of the tray assembly of the cell culture system of FIG. 52. [Figure 56] FIG. 56 is a side view of the tray assembly of FIG. 55. [Figure 57] FIG. 56 is a top view of the tray of the tray assembly of FIG. 55. [Figure 58] FIG. 1 is a front view of a pair of incubators with multiple cell culture systems arranged on shelves therein. [Figure 59] FIG. 1 is a system diagram showing an exemplary fluidic setup within the system during cell culture treatment. [Figure 60] 59. FIG. 60 is a table showing the contents shown in FIG. 59. [Figure 61A] Included is a table showing examples of cell passaging procedures. [Figure 61B] Included is a table showing examples of cell passaging procedures. [Figure 62] 4A to 4C show container lids according to embodiments. [Figure 63A] FIG. 1 is a top view of a multi-port valve, according to an embodiment. [Figure 63B]FIG. 63B is a bottom view of the multiport valve of FIG. 63A. [Figure 63C] FIG. 63B is a side view of the multiport valve of FIG. 63A; [Figure 63D] FIG. 63D is a cross-sectional view taken along line 63D-63D in FIG. 63C. [Figure 64A] FIG. 63B is a cross-sectional view of the valve body of the multiport valve of FIGS. 63A to 63D. [Figure 64B] FIG. [Figure 64C] FIG. 64B is a cross-sectional side view of the valve body of FIG. 64A. [Figure 65] 63A, B is a cross-sectional view taken along line 65B-65B in A, and C is a top view of the valve rotor. DETAILED DESCRIPTION OF THE INVENTION

[0015] In some embodiments, the device includes a tray, a first lid, a second lid, and a multi-port valve. The tray is configured to be removably coupled to a housing of a base unit. The tray has a first coupler configured to couple a first container to the tray and a second coupler configured to couple a second container to the tray. The first lid is configured to couple to a first container and includes a first liquid exchange port and a first gas exchange port. The second lid is configured to couple to a second container and includes a second liquid exchange port and a second gas exchange port. The multi-port valve is coupled to the tray and includes a master port and a set of selectable ports. The multi-port valve engages with a valve actuator of the base unit and is configured to couple to a fluid pump coupled to the base unit. A first selectable port of the set of selectable ports is aseptically coupled to a first liquid exchange port of the first lid. A second selectable port of the set of selectable ports is aseptically coupled to a second liquid exchange port of the second lid.

[0016] In some embodiments, the first coupler maintains the first container in a fixed position on the tray during operation of the device, and the second coupler maintains the second container in a fixed position on the tray. In some embodiments, the first container is a cell culture container configured to receive a cell sample, and the second container is one of a waste container, a reagent container, or a cell collection container. In some embodiments, the first coupler is configured to removably couple the cell culture container to the tray. In some embodiments, the cell culture container and the tray each include a transparent portion. The first coupler is configured to couple the cell culture container to the tray such that the transparent portion of the cell culture container aligns with the transparent portion of the tray.

[0017] In some embodiments, the multiport valve and fluid pump are configured to transfer fluid between a first container and a second container within a closed sterile system. In some embodiments, the multiport valve is configured to be removably coupled to the tray and to be removably coupled to a valve actuator of a base unit. In some embodiments, the pump includes a pump actuator and a pump body defining a pump chamber. The pump body is configured to couple to a master port of the multiport valve.

[0018] In some embodiments, the tray is configured to engage an agitator coupled to the base unit, the agitator configured to agitate the tray when activated.

[0019] In some embodiments, the apparatus includes a counting chip coupled to the tray and coupled to a third selectable port of the multiport valve, the counting chip configured to receive a portion of the cell sample mixture from the first container at periodic time intervals.

[0020] In some embodiments, the tray, the first lid, the second lid, and the multiport valve are enclosed in a wrap. In some embodiments, the tray, the first lid, the second lid, and the multiport valve are sterilized within the wrap.

[0021] In some embodiments, the base unit of the cell culture system includes a housing, a pump actuator, and a valve actuator. The housing defines (or includes) a receiving portion configured to removably receive a cell culture tray assembly. The cell culture tray assembly includes a tray, a first lid coupled to the tray that can be removably coupled to a first container, and a second lid coupled to the tray that can be removably coupled to a second container. The first lid and the second lid each include a liquid exchange port and a gas exchange port. The cell culture tray also includes a multiport valve coupled to the tray and including a master port and a set of selectable ports. The pump actuator is coupled to the housing and configured to be operably coupled to a fluid pump coupled to the master port of the multiport valve. The valve actuator is coupled to the housing and configured to be coupled to the multiport valve when the cell culture tray assembly is coupled to the receiving portion of the housing. The valve actuator and the pump actuator are collectively configured to selectively move fluid into and out of a first container coupled to the first lid and into and out of a second container coupled to the second lid.

[0022] In some embodiments, the multiport valve is configured to be removed from the tray and coupled to a valve actuator while a first port of the multiport valve is aseptically coupled to a first lid and a second port of the multiport valve is aseptically coupled to a second lid. In some embodiments, the valve actuator includes a keyed drive member configured to matingly engage with the multiport valve.

[0023] In some embodiments, the fluid pump is sterilely connected to the master port of the multiport valve via a length of tubing, hi some embodiments, the fluid pump is one of a piston pump, a peristaltic pump, or a vane pump.

[0024] In some embodiments, the base unit further includes an agitator coupled to the housing and configured to engage the cell culture tray assembly when the cell culture assembly is coupled to the housing. The agitator is configured to agitate the cell culture tray assembly when activated. In some embodiments, the receiving portion of the housing includes a support plate coupled to the agitator. The support plate includes a surface to which the cell culture tray assembly can be removably coupled.

[0025] In some embodiments, the base unit further includes (or is coupled to) an electronic (or computer) control system configured to control fluid movement into and out of the first container coupled to the first lid and into and out of the second container coupled to the second lid. In some embodiments, the base unit includes a sensor movably coupled to the housing and configured to generate a cell signal related to a quantity of cells in the first container. In some embodiments, the sensor is an imaging device coupled to the housing and configured to image the contents in the first container so that at least one of the confluence or density of the cells in the first container can be determined. In some embodiments, the sensor is configured to monitor the color of the contents of the first container. The first container can include a color-based pH indicator so that the pH of the contents of the first container can be determined.

[0026] In some embodiments, the base unit of the cell culture system includes a housing, a pump actuator, a valve actuator, and an electronic control system. The housing defines a receiving portion configured to removably receive a cell culture tray assembly. The cell culture tray assembly includes a tray, a first lid coupled to the tray that can be removably coupled to a first container, and a second lid coupled to the tray that can be removably coupled to a second container. The cell culture tray also includes a multiport valve coupled to the tray and including a master port and a set of selectable ports. The pump actuator is coupled to the housing and configured to be operably coupled to a fluid pump. The valve actuator is coupled to the housing and configured to be coupled to the multiport valve when the cell culture tray assembly is coupled to the receiving portion of the housing. The valve actuator and the pump actuator are collectively configured to selectively move fluid into and out of the first container coupled to the first lid and into and out of the second container coupled to the second lid. The electronic control system includes a cell sensor, a cell sensor module, and an actuator module. The cell sensor is configured to generate an output associated with the contents in the first container. The cell sensor module is implemented in at least one of a memory or processing device of the electronic control system and generates a cell signal associated with a quantity of cells in the first container based on the output of the cell sensor. The actuator module is implemented in at least one of the memory or processing device and receives the cell signal and generates at least one of a valve control signal or a pump signal based on the cell signal to move the cells out of the first container.

[0027] In some embodiments, the actuator module is configured to control the movement of a first volume of fluid from the first container to a waste container and the movement of a second volume of fluid from a reagent container to the first container, hi some embodiments, the actuator module is configured to control the movement of a volume of enzyme into the first container to promote cell dissociation of adherent cells in the first container.

[0028] In some embodiments, the apparatus includes an agitator coupled to the housing and configured to engage the tray assembly when the tray assembly is coupled to the receiving portion. The agitator is configured to agitate the tray assembly. An actuator module of the electronic control system is configured to control actuation of the agitator (e.g., when to agitate and the duration of agitation).

[0029] In some embodiments, the cell sensor is movably coupled to the housing, and the sensor module is configured to control movement of the cell sensor relative to the housing such that the cell sensor can be aligned with the first container.

[0030] In some embodiments, the base unit includes a valve sensor configured to generate a valve position signal related to a rotational position of a valve actuator. The valve position signal indicates that one of the selectable ports of the multiport valve has been selected. The actuator module is configured to generate a valve control signal based in part on the valve position signal. In some embodiments, the base unit includes a pump sensor configured to generate a pump signal related to a position of the pump actuator during operation. The actuator module is configured to generate a pump control signal based in part on the pump signal.

[0031] In some embodiments, the electronic control system further includes a radio configured to electronically communicate with the computing device, the radio configured to transmit a wireless signal to the computing device related to a measurement related to the amount of cells in the first container.

[0032] In some embodiments, a base unit of a cell culture system includes a housing, a pump actuator, a valve actuator, and an electronic control system. The housing defines a receiving portion configured to removably receive a cell culture tray assembly. The cell culture tray assembly includes a tray, a first cell culture container, a second cell culture container, a reagent container, a waste container, and a multiport valve. The multiport valve includes a master port and a set of selectable ports. The first selectable port is coupled to the first cell culture container, the second selectable port is coupled to the second cell culture container, the third selectable port is coupled to the reagent container, and the fourth selectable port is coupled to the waste container. The pump actuator is coupled to the housing and configured to be operably coupled to a fluid pump coupled to the master port of the multiport valve. The valve actuator is coupled to the housing and configured to be coupled to the multiport valve. The electronic control system is operably coupled to the valve actuator and the pump actuator. The electronic control system includes an actuator module implemented in at least one of a memory or a processing device and configured to generate a series of valve control signals and pump control signals. Specifically, the actuator module can generate a first valve control signal to cause the valve actuator to actuate the multiport valve and a first pump control signal to cause the pump actuator to actuate a fluid pump to move cell culture medium from the first cell culture container to the waste container. The actuator module can generate a second valve control signal to cause the valve actuator to actuate the multiport valve and a second pump control signal to cause the pump actuator to actuate a fluid pump to move reagent from the reagent container to the first cell culture container. The actuator module can generate a third valve control signal to cause the valve actuator to actuate the multiport valve and a third pump control signal to cause the pump actuator to actuate a fluid pump to move a plurality of cells from the first cell culture container to the second cell culture container.

[0033] In some embodiments, the electronic control system includes a cell sensor module implemented in at least one of a memory or a processing device. The cell sensor module receives an output from the cell sensor and generates a cell signal indicative of dissociation of the cells in the first cell culture vessel. The actuator module is configured to generate at least one of a third valve control signal or a third pump control signal in response to the cell signal. In some embodiments, the cell sensor is a microscope, and the output from the microscope is an image. The cell sensor module is configured to generate the cell signal indicative of dissociation of the cells based on the image. In some embodiments, the cell sensor module is configured to generate an alignment signal to move the cell sensor into alignment with the first cell culture vessel.

[0034] In some embodiments, the base unit includes an agitator coupled to the housing and configured to engage the tray assembly, the agitator configured to agitate the tray assembly, and an actuator module of the electronic control system configured to generate an agitation signal that causes the agitation of the tray assembly.

[0035] In some embodiments, the computer-implemented method includes receiving, at an electronic control system of the cell culture assembly, a sensor output from a sensor of the cell culture assembly. The cell culture assembly includes a disposable cell culture tray assembly connectable to a reusable base unit. The cell culture tray assembly includes a tray, a first lid connected to a first container, a second lid connected to a second container, and a multi-port valve connected to the tray. The multi-port valve includes a plurality of selectable ports and a master port connected to a fluid pump. At least one of the first container or the second container contains a plurality of cells. A cell signal related to a quantity of the plurality of cells in one of the first container and the second container is generated based on the sensor output. Based on the cell signal, at least one of a valve control signal for operating the multi-port valve or a pump control signal for operating the fluid pump is generated by the electronic control system to initiate fluid flow from at least one of the first containers.

[0036] In some embodiments, the sensor is part of an optical measurement assembly configured to move the sensor, and the method further includes transmitting a position signal to the optical measurement assembly to move the sensor to a measurement position relative to at least one of the first container or the second container. In some embodiments, the cell sensor is a microscope, and the sensor output from the microscope is an image. The electronic control system can generate a cell signal indicative of dissociation of the cells in the first container or the second container based on the image.

[0037] In some embodiments, the base unit includes an agitator operably coupled to a tray of the tray assembly. The method optionally includes sending an agitator signal from the electronic control system to the agitator to activate agitation of the tray assembly to maintain the cells in suspension in at least one of the first container or the second container. In some embodiments, the method includes, after sending the agitator signal, sending at least one of an actuator signal or a pump signal to cause flow of the fluid mixture from one of the first container and the second container to a counting chip fluidically coupled to one of the first container and the second container.

[0038] In some embodiments, a computer-implemented method can control fluid movement within a cell culture assembly including a disposable cell culture tray assembly coupled to a reusable base unit. The method includes generating a first valve control signal and a first pump control signal via an actuator module of an electronic control system of the cell culture assembly. The first valve control signal causes a valve actuator of the base unit to actuate a multiport valve to fluidly couple a first selectable port of the multiport valve to a master port of the multiport valve. The master port is fluidly coupled to a fluid pump, with each selectable port fluidly coupled to one of a first cell culture container, a second cell culture container, a reagent container, or a waste container. The first pump control signal causes a pump actuator of the base unit to actuate a fluid pump to move cell culture medium from the first cell culture container to the waste container. A second valve control signal is generated, causing the valve actuator to actuate the multiport valve to fluidly couple a second selectable port to the master port, and the second pump control signal causes the pump actuator to actuate a fluid pump to move reagent from the reagent container to the first cell culture container. A third valve control signal is generated causing the valve actuator to actuate the multiport valve to fluidly connect the third selectable port to the master port, and a third pump control signal causes the pump actuator to actuate the fluid pump to move the plurality of cells from the first cell culture container to the second cell culture container.

[0039] In some embodiments, the method includes generating, via the actuator module, a fourth valve control signal to a valve actuator to actuate the multiport valve and fluidly connect the fourth selectable port to the master port, and a fourth pump control signal to a pump actuator to actuate a fluid pump to move the wash medium from the wash container to one of the multiport valve, a holder, or a tube connected to the multiport valve, or a cell incubator.

[0040] In some embodiments, the base unit includes a cell sensor, and the method includes receiving an output from the cell sensor. A cell signal indicative of dissociation of cells in the first cell culture container is generated. The actuator module generates at least one of a third valve control signal or a third pump control signal in response to the cell signal. In some embodiments, the method includes generating an alignment signal to move the cell sensor into alignment with the first cell culture container.

[0041] In some embodiments, a computer-implemented method can control fluid movement in a cell culture assembly based on measured or calculated amounts of fluid in one or more containers. The cell culture assembly includes a disposable cell culture tray assembly coupled to a reusable base unit. The method includes generating a first valve control signal and a first pump control signal via an actuator module of an electronic control system of the cell culture assembly. The first valve control signal causes a valve actuator of the base unit to actuate a multiport valve to fluidly connect a first selectable port of the multiport valve to a master port of the multiport valve. The master port is fluidly connected to a fluid pump. Each selectable port is fluidly connected to one of a cell culture container, a second cell culture container, or a cell culture medium container. The first pump control signal causes a pump actuator of the base unit to actuate a fluid pump to move a first volume of cell culture medium from the cell culture medium container to the first cell culture container. A volume of liquid in the first cell culture container is determined. The method includes generating, via the actuator module, a second valve control signal and a second pump control signal when the volume of fluid is below a threshold volume. The second valve control signal causes the valve actuator to actuate a valve or otherwise maintain fluid communication between the first selectable port and the master port of the multiport valve. The second pump control signal causes the pump actuator of the base unit to actuate a fluid pump to move a second volume of cell culture medium from the cell culture medium container to the first cell culture container. The method includes generating, via the actuator module, a third valve control signal and a third pump control signal when the volume of fluid exceeds a threshold volume. The third valve control signal causes the valve actuator to actuate the multiport valve to fluidly connect a second selectable port of the plurality of selectable ports to the master port of the multiport valve. The third pump control signal causes the pump actuator of the base unit to actuate the fluid pump to move a plurality of cells from the first cell culture container to the second cell culture container.

[0042] In some embodiments, the method includes removing a cell culture tray assembly from an outer protective wrap. The tray assembly includes a tray, a first lid, a second lid, and a multi-port valve. The first lid is coupled to the tray and configured to be removably coupled to a first container. The first lid includes a first liquid exchange port and a first gas exchange port. The second lid is coupled to the tray and configured to be removably coupled to a second container. The second lid includes a second liquid exchange port and a second gas exchange port. The multi-port valve is coupled to the tray and includes a master port and a plurality of selectable ports. A first selectable port of the plurality of selectable ports is aseptically coupled to a first liquid exchange port of the first lid, and a second selectable port of the plurality of selectable ports is aseptically coupled to a second liquid exchange port of the second lid. At least one cell is added to the first container through an opening in the first container. The first lid is secured to the first container to close the opening. The tray assembly is coupled to a base unit, a valve actuator of the base unit engages the multiport valve of the tray assembly after or simultaneously with coupling the tray assembly to the base unit, and a fluid pump is coupled to the pump actuator of the base unit.

[0043] In some embodiments, the method includes connecting the tray assembly and connecting the fluid pump, and then moving the base unit with the connected tray assembly to the incubation environment. In some embodiments, the method includes removing the multiport valve from the tray assembly and connecting the multiport valve to the base unit such that a valve actuator of the base unit matingly engages with the multiport valve. In some embodiments, removing the multiport valve is performed while a first selectable port of the multiport valve is aseptically connected to a first lid and a second selectable port of the multiport valve is aseptically connected to a second lid. In some embodiments, the removing, adding, and securing are performed in a sterile environment. In some embodiments, before securing the first lid to the first container, a volume of reagent and at least one cell are added to the first container. In some embodiments, after securing the first lid to the first container, the first container is connected to a coupler of the tray assembly. In some embodiments, the method further includes connecting a fluid pump to a port of the multiport valve via a tube. In some embodiments, coupling the fluid pump to the multi-port valve includes coupling a master port of the multi-port valve to the fluid pump via a tube.

[0044] When used in connection with a referenced numerical indication, the term "about" means the referenced numerical indication plus or minus up to 10% of the referenced numerical indication. For example, "about 100" means 90 to 110. The term "substantially," when used in connection with, for example, a geometric relationship, a numerical value, and / or a range, is intended to convey that the geometric relationship (or structure described thereby), numerical value, and / or range so defined is nominally the recited geometric relationship, numerical value, and / or range. For example, two structures described herein as "substantially parallel" are intended to convey that while a parallel geometric relationship is desired, some non-parallelism may occur in a "substantially parallel" arrangement. As another example, a structure defining a volume that is "substantially 0.50 milliliters (mL)" is intended to convey that the specified volume is desired, but that some tolerance may occur when the volume is "substantially" the specified volume (e.g., 0.50 mL). Such tolerances may arise from manufacturing tolerances, measurement tolerances, and / or other practical considerations (e.g., minor imperfections, age of the structure so defined, pressures or forces exerted within the system, etc.) As noted above, a suitable tolerance may be, for example, ±10% of a described geometry, value, and / or range.

[0045] As used herein, the term "reagent" includes any substance used in connection with any of the reactions described herein. For example, reagents can include buffers, enzymes, cell culture media, wash solutions, etc. A reagent can include a mixture of one or more components. A reagent can include such components regardless of the state of matter (solid, liquid, gas, etc.). Furthermore, a reagent can include multiple components that can be contained in a mixed, unmixed, and / or partially mixed state of matter. A reagent can include both active and inactive components. Thus, as used herein, a reagent can include non-active and / or inactive components such as water, colorants, etc.

[0046] As used herein, the term "set" can refer to multiple features or a single feature with multiple portions. For example, when referring to a set of walls, the set of walls can be considered as one wall with multiple portions, or the set of walls can be considered as multiple separate walls. Thus, a monolithically constructed item can include a set of walls. Such a set of walls can include, for example, multiple portions that are contiguous or discontinuous with one another. A set of walls can also be fabricated from multiple items that are fabricated separately and later connected together (e.g., via welding, adhesive, or any suitable method).

[0047] FIG. 1A shows a schematic diagram of an automated cell culture system according to an embodiment. This exemplary automated cell culture system 100 has three cell culture vessels 111, 113, and 115. These vessels may be, for example, laboratory flasks or dishes. The cell culture vessels hold cell cultures, growth media, and any other additives or reagents related to cell culture. The cell cultures in the vessels may be any type of adherent or suspension cell culture.

[0048] Fluid pumps 103 and 105 are single-port fluid pumps that contain an internal fluid reservoir. An example of a single-port fluid pump is a syringe mated to a syringe driver. A syringe fluid pump can draw fluid into its internal reservoir by creating suction on the reservoir by withdrawing the syringe plunger. Similarly, a syringe pump can expel liquid from the reservoir by pushing the plunger back into the syringe. In other embodiments, one or both of fluid pumps 103, 105 can include a bidirectional in-line pump with separate reservoirs. A bidirectional pump can be, for example, a peristaltic pump or an impeller-based fluid pump that can pump fluid in two directions along a fluid channel. A bidirectional in-line pump can be fitted with a dedicated reservoir on one end and used as an input and output port on the other end in a manner similar to a syringe pump. The dedicated reservoir fitted to the pump may be flexible and sealed, such as a bag or pouch, so that air pockets do not form within the reservoir when fluid is pumped out of the reservoir.

[0049] Fluid pumps 103 and 105 are fluidly connected to multiport valves 107 and 109, respectively. Multiport valves 107 and 109 have one master port and multiple selectable ports. The multiport valves can selectively fluidly connect the master port to one of the selectable ports at a time. When the master port of the multiport valve is connected to the selected port, the other selectable ports are sealed and not fluidly connected to the master port. When the master port of the multiport valve is fluidly connected to the selectable ports, fluid can flow in either direction through the valve. That is, fluid can enter the multiport valve through the master port and exit through the selected port, or fluid can flow in the opposite direction, entering the multiport valve through the selected port and exiting through the master port. In some embodiments, the multiport valve can be a mechanical valve device; in other embodiments, the multiport valve can be constructed from microfluidic chip components.

[0050] Fluid pumps 103 and 105, multiport valves 107 and 190, and cell incubators 111, 113, and 115 are all fluidly connected to one another by fluidic channels. In embodiments, the fluidic channels are comprised of flexible tubing. In other embodiments, some or all of the fluidic channels may be rigid tubing or channels within the substrate. In the example shown in FIG. 1A, fluid pump 103 is fluidly connected to the master port of multiport valve 107 by flexible tubing. Multiport port 107 has several selectable ports 107a-d. Selectable port 107a is fluidly connected to cell incubator 111, selectable port 107b is fluidly connected to cell incubator 113, and selectable port 107c is fluidly connected to cell incubator 115. Selectable port 107d is fluidly connected to reservoir 119. Reservoir 119 may be any type of fluid reservoir for supplying fluid to or receiving fluid from the automated cell culture system. For example, container 119 may be a waste container for receiving waste from an automated cell culture system. In another example, container 119 may contain fresh cell culture medium for supplying fresh medium to a cell incubator.

[0051] Fluid pump 105, multiport valve 109, and container 117 are configured similarly to fluid pump 103, multiport valve 107, and container 119. Multiport 109 has several selectable ports 109a-d. Selectable port 109a is fluidly connected to cell incubator 111, selectable port 109b is fluidly connected to cell incubator 113, and selectable port 109c is fluidly connected to cell incubator 115. Selectable port 109d is fluidly connected to container 117.

[0052] In operation, the combination of fluid pumps, multiport valves, reservoirs, and cell incubators in the example shown in FIG. 1A can be used to transfer fluids between the cell incubators and reservoirs. In some embodiments, a first fluid pump 103 is used to add medium to the cell incubator from reservoir 119, and a second fluid pump 105 is used to remove medium from the cell incubator to reservoir 117. In another embodiment, a single fluid pump is used for both adding and removing medium from the cell incubator. In some embodiments, the components of group 101, including cell incubators 111, 113, 115 and multiport valves 107 and 109, can be separable from fluid pumps 103 and 105 and reservoirs 117 and 119. Fluid connections between components within group 101 can be established independently in a first stage of assembly, after which additional components can be connected at a later stage. The components of group 101 can be sterilized or processed independently in a first stage and then introduced to the remaining components in a second stage. Fluid connections between components of group 101 and other components can be made with sterile connections so that contaminants are not introduced into the sterilized components of group 101. Cell culture vessels 111, 113, 115 can be connected to valves 107 and 109 using tubing and sterile connections so that the vessels can be aseptically disconnected from the system when the cells therein are removed for use or analysis.

[0053] FIG. 1B shows a schematic diagram of an automated cell culture system according to an embodiment. The automated cell culture system 110 includes one bidirectional fluid pump 121. In this embodiment, the cell incubators 111, 113, and 115, the multiport valves 107 and 109, and the vessels 117 and 119 are the same as those described in connection with FIG. 1A. In FIG. 1B, the fluid pump 121 is a two-port fluid pump, such as a peristaltic pump. A first port 121a of the two-port fluid pump 121 is fluidly connected to the master port of the multiport valve 107, and a second port 121b of the fluid pump 121 is fluidly connected to the master port of the multiport valve 109. The fluid pump 121 can pump fluid in two directions. In a first mode of operation, the fluid pump 121 pumps fluid from port 121a to port 121b, and in a second mode of operation, the fluid pump 121 pumps fluid from port 121b to port 121a.

[0054] FIG. 2 shows a top view of an automated cell culture system according to an embodiment. Automated cell culture system 200 includes two fluid pumps, two multiport valves, and twelve cell culture vessels. For clarity, the illustrated example does not include fluid connections; however, it is understood that at least some of the various components of the automated cell culture system are fluidly connected during use. Removable tray 223 includes cell culture vessels 201-212 and multiport valves 213 and 215. Each cell culture vessel is covered by a sterile lid, such as sterile lid 237, which covers cell culture vessel 206. Each cell culture vessel is removably attached to removable tray 223 by brackets, such as brackets 217, 219, and 221, which hold cell culture vessel 206. Removable tray 223 is removably inserted into base housing 235 and guided by guides 225a-f. Base housing 235 includes two syringe-style fluid pumps. The first fluid pump consists of a syringe 229 and a syringe actuator 227. The syringe actuator 227 pushes or pulls the plunger of the syringe 229, resulting in fluid flow into and out of the syringe. In an embodiment, the syringe actuator is a linear actuator, although any other method of pushing or pulling the syringe plunger can be used. The second pump consists of a syringe 233 and a syringe actuator 231.

[0055] 3A shows a top view of a base housing of an automated cell culture system, according to an embodiment. The illustrated exemplary base housing 301 includes fluid pumps 305 and 307 and multiport valve actuators 309 and 311. The base housing 301 also includes a controller that controls the operation of the fluid pumps, multiport valves, and any other systems, such as an automated cell counter system, a hemocytometer, an imaging system, a microscope, or other measurement or analysis system for facilitating automated cell growth. The controller may include one or more processors configured to execute instructions contained in one or more memory systems to control the automated cell culture system and other corresponding systems. Additionally, the controller may include one or more network interfaces through which various notifications or data transfers may be sent or received.

[0056] 3B illustrates a removable tray assembly of an automated cell culture system according to an embodiment. The removable tray assembly 303 is configured to fit into the base housing 301. When the removable tray assembly 303 is placed on top of the base housing 301, the multiport valve actuators 309 and 311 mechanically couple to the multiport valves 319 and 321, respectively. For example, in an embodiment, the multiport valve actuator 309 rotates an internal member of the multiport valve 319 to align the master port of the multiport valve 319 with one of the selectable ports 319a-d. The multiport valves 319 and 321 and the cell culture vessels 313, 315, and 317 are carried on the removable tray 303. When the base housing 301 and the removable tray 303 are combined, the fluid pumps 305 and 307 can be fluidly connected to the master ports of the multiport valves 319 and 321.

[0057] In some embodiments, the base housing 301 may also include an agitator configured to agitate the removable tray assembly 303 relative to the base housing. The agitator may agitate the tray with a rocking, vibrating, circular, orbital motion, or other motion useful for culturing cells. In some embodiments, individual cell culture vessels may be independently agitated by an independent agitator disposed between the cell culture vessel and the removable tray. Independent agitators may be used in applications where agitation of all cell culture vessels in a tray is disadvantageous when only a subset of the cell culture vessels requires agitation. In some embodiments, the independent agitator may be integrated into one or more brackets used to secure the cell culture vessel to the removable tray. In some embodiments, the agitator may have an active component disposed within the base housing that mechanically couples to a passive component on the removable tray, similar to how a multiport valve on a removable tray mechanically mates to an actuator within the base housing.

[0058] During use, the removable tray 303 can be configured with any number or configuration of multiport valves, cell incubators, and fluid tubing, as needed, separate from the base housing 301. The removable tray 303 and its associated components can then be sealed and sterilized before being introduced into the base housing 310. In some embodiments, the cell incubator can be added to the tray 303 in a sterile environment after sterilization of the tray 303. Because the base housing 301 can remain stationary and the base housing components are not in fluid contact with the sterile system above the removable tray 303, any electromechanical components, such as valve actuators or pump mechanisms, located within the base housing do not need to undergo transport or sterilization procedures. When using a syringe-style fluid pump, a sterile syringe can be placed in the syringe actuator and used to prevent the syringe actuator from coming into contact with any fluid in the sterile system. Similarly, a peristaltic pump can use a sterile section of tubing so that stationary components associated with the base housing do not fluidly contact the sterile system.

[0059] 4 illustrates an exemplary removable tray of an automated cell culture system mated to an exemplary base housing, according to an embodiment. As shown in this example, automated cell culture system 400 includes removable tray 140 and base housing 403. Removable tray 401 includes multiport valves 405 and 407 and cell incubators 409, 411, and 413. Removable tray 401 is lowered onto base housing 403, aligning multiport valve actuators 415 and 417 with multiport valves 405 and 407, respectively. When removable tray 140 is lowered onto base housing 403, multiport valve actuators 415 and 417 mechanically couple with multiport valves 405 and 407. After the two components are coupled, fluid pumps 419 and 421 are fluidly connected to multiport valves 405 and 407 mounted on the removable tray, such as by a manual connection step.

[0060] 5 illustrates a cross-sectional view of an exemplary multi-port valve, according to an embodiment. In this embodiment, multi-port valve 500 includes a valve body 503 having a master port 507 on its top surface and multiple selectable ports 505 and 509 distributed around its periphery. Two selectable ports are shown in this cross-sectional view. However, it should be understood that various embodiments of the multi-port valve can include any number of selectable ports.

[0061] The valve body 503 has a cylindrical cavity on its underside into which the rotatable cylindrical valve rotor 501 is inserted. Within the rotatable cylindrical valve rotor 501 is a fluid channel 517 that fluidly connects the axial master port of the rotatable cylindrical valve rotor 501 to the radial master port of the rotatable cylindrical valve rotor 501. Within the valve body 503 is a fluid channel 513 that fluidly connects the master port 507 to the fluid channel 517 of the rotatable cylindrical valve rotor 501. The connection between the fluid channel 513 and the fluid channel 517 remains constant while the rotatable cylindrical valve rotor 501 rotates because both fluid channels are centered on the axis of rotation of the rotatable cylindrical valve rotor 501 within the cylindrical cavity of the valve body 503.

[0062] 5 , rotatable cylindrical valve rotor 501 is rotated so that fluid channel 511 is aligned with fluid channel 517. Thus, a fluid circuit is established from master port 507, through fluid channel 513, fluid channel 517, and fluid channel 511, to selectable port 505. In this illustrated state, fluid channel 515 and then selectable port 509 are sealed by the presence of a solid portion of rotatable cylindrical valve rotor 501. In operation, rotatable cylindrical valve rotor 501 can rotate to establish a fluid path from master port 507 to selectable port 509 while sealing selectable port 505 and fluid channel 511.

[0063] The multiport valve 500 can be made of any suitable material, and the valve body 503 and valve rotor 501 can be made of the same or different materials. Examples of materials that can be used include plastic, TFE-based materials such as polytetrafluoroethylene (PTFE), metal, rubber, or similar materials. In some embodiments, the valve body 503 and valve rotor 501 can be machined to fit within very close tolerances, resulting in a fluid-tight seal between the two components. In some embodiments, additional gaskets, bearings, seals, and / or flanges can be incorporated into the multiport valve 500 to provide a fluid-tight connection between the valve body 503 and the valve rotor 501.

[0064] FIG. 6A shows an example of an exemplary multiport valve according to an embodiment. In this example, multiport valve 600 has axial port 601 and eight selectable ports, four of which (ports 603, 605, 607, and 609) are visible in the perspective view of FIG. 6A. FIG. 6B shows a bottom view of multiport valve 600 showing mechanical coupler 611 configured to mechanically couple to a multiport valve actuator. The corresponding multiport valve actuator has a cavity shaped to receive mechanical coupler 611 and transfer rotational mechanical energy to multiport valve 600.

[0065] FIG. 7 illustrates a sterile cell incubator lid according to an embodiment. In this exemplary embodiment, cell incubator lid 703 is attached to cell incubator 701. In this exemplary embodiment, cell incubator lid 703 has three ports 705, 707, and 709. In this example, the three ports are arranged vertically. When cell incubator 701 is filled with liquid, such as cell growth medium, a tube entering through the lowest port 709 may be submerged in the liquid, and the tube can be used to siphon the liquid through port 709. The tube entering through the middle port, port 707, can be positioned so that the tube is not in liquid contact with the contents of the cell incubator, allowing additional liquid to be added to the cell growth device without contaminating the fluid path to port 707. Port 705 can be configured to allow gas exchange in and out of cell growth device 701. In some embodiments, port 705 can be configured to allow gas to be circulated through the cell growth device. sterile The incubation chamber includes a filter for filtering gases on their way into the flask for cell culture. In some applications, an automated cell culture system can be placed in the incubation chamber to regulate the environment proximate to the cell incubator. The incubation chamber, in some embodiments, can be integrated with the base housing of the automated cell culture system. In one embodiment, the regulated environmental characteristics include the gas mixture, temperature, and humidity level. In one embodiment, the incubation chamber regulates the gas mixture, temperature, and humidity level depending on the cell line being grown. In some embodiments, port 705 can be attached to an environmental conditioning device that manages the temperature, humidity, oxygenation, gas mixture, and other such parameters of the gaseous environment inside the cell incubator. The sterile lid can be made to fit any cell incubator used in manual cell culture, allowing the system to be integrated with any incubator.

[0066] 8 shows a cross-sectional view of a cell incubator lid according to an embodiment. Cell incubator lid 803 is threaded onto the port of cell incubator 801 such that the threads on cell incubator lid 803 engage with the threads on the port of cell incubator 801. In this exemplary embodiment, cell culture lid 803 has liquid port 807 and gas port 811. Liquid channel 809 is threadably engaged with liquid port 807. Gas filter 805 is threadably engaged with gas port 811. Gas filter 805 may allow gas exchange in and out of the cell incubator while preventing any microorganisms or pathogens from entering the cell incubator from the outside. In an embodiment, gas filter 805 is a 0.22 micron filter.

[0067] FIG. 9 illustrates steps of a method for transferring a liquid from a first vessel to a second vessel using an automated cell culture system with a single-port pump, according to an embodiment. In this example, the automated cell culture system has a single-port pump, such as the syringe-type pump described above, or a two-port pump with a retainer attached to one port. This method can be used to transfer liquid from any vessel to another. For example, the first vessel can be a cell culture vessel and the second vessel can be a waste container. In another example, the first vessel can be a container of fresh cell growth medium and the second vessel can be a cell culture vessel.

[0068] In Figure 9, in step 901, a multi-port valve with a master port connected to a single-port pump or a two-port pump with a retainer is configured to select a selectable port in fluid communication with a first vessel. In step 902, the single-port pump is activated to draw fluid from the first vessel into a reservoir of the single-port pump, or similarly, the two-port pump is activated to draw fluid into the retainer. Next, in step 903, the multi-port valve is configured to select a selectable port in fluid communication with a second vessel. Next, in step 904, fluid is pumped from the reservoir of the single-port pump, or similarly, from the retainer by the two-port pump, through the configured multi-port valve and into the second vessel.

[0069] Some embodiments of automated cell culture systems can use a two-port pump with a multi-port valve fluidly connected to each port. The two-port pump can be unidirectional or bidirectional. A two-port pump does not need to transfer liquid to a holding reservoir like a single-port pump, but can pump directly from one vessel to another. FIG. 10 shows steps of a method for transferring liquid from a first vessel to a second vessel using an automated cell culture system with a two-port pump, according to an embodiment. In this example, a first port of the two-port pump is fluidly connected to a master port of a multi-port valve, and a second port of the two-port pump is fluidly connected to the master port of the multi-port valve. In step 1001, the first multi-port valve is configured to select a selectable port in fluid communication with the first vessel. In step 1002, the second multi-port valve is configured to select a selectable port in fluid communication with the second vessel. Finally, in step 1003, the two-port pump is activated to pump in the direction of the first port towards the second port so that liquid from the first vessel is pumped into the second vessel.

[0070] For any embodiment disclosed herein, a simple reference to pumping from a first vessel to a second vessel may refer to alternatives in an appropriate manner depending on whether the automated cell culture system is configured with a one-port pump or a two-port pump. Some embodiments of the automated cell culture system may also combine two-port and single-port pumps in a single system, such that one step of pumping uses one type of pump and another step of pumping uses a different type of pump.

[0071] In some embodiments, for example, when signs of differentiation are observed for stem cells, media from different sources can be supplied to the cells depending on the observed state of the cells. In embodiments, the first step of the method is to observe the state of the cells, such as signs of differentiation in stem cells. The first step can be performed by a microscope, camera, or other measuring device. The second step of the method is to select an appropriate media source based on the state of the cells. The third step of the method is to operate a one-port or two-port pump system to transfer media from the selected media source to a vessel containing the cells.

[0072] In some embodiments, the automated cell culture system includes a microscope that can be moved to image the contents of any cell culture vessel in the automated cell culture system. In some examples, the microscope can be attached to a mechanical system that can move the microscope to the cell culture vessel, such as a two-dimensional or three-dimensional gantry mechanism or a hinged robotic arm mechanism. In some embodiments, the microscope can remain stationary while the automated cell culture system is moved to position individual cell culture vessels in view of the stationary microscope. In some embodiments, the microscope and movable assembly can be contained within the base housing of the automated cell culture system, so that the cell culture vessels can be imaged from their underside. In such embodiments, the removable tray that holds the cell culture vessels can have a transparent window or cutout below the cell culture vessel to allow the microscope to image the cells contained therein. In some embodiments, an adjustable and controllable light source is positioned on the opposite side of the cell culture vessel as the microscope to provide light to the microscope. For example, the light source, like the microscope, can be attached to a mechanical system that can move the light source to any cell culture vessel as needed. In some embodiments, a stationary light source can be positioned to one side of the automated cell culture system so that each cell culture vessel is sufficiently illuminated.

[0073] The automated cell culture system may also include other imaging devices. For example, the automated cell culture system may include one or more cameras or LED and light sensor pairs to image the contents of the cell culture vessel. This type of imager may be useful for measuring and monitoring macro-level visual characteristics of the cell culture vessel. For example, a color camera or LED and light sensor pair may be useful for monitoring the color of the contents of a cell culture vessel containing a color-based pH indicator, such as phenol red, thereby determining the pH of the cell culture vessel contents. In embodiments, each cell culture vessel bracket may include a camera for imaging the contents of the cell culture vessel. In another embodiment, a single camera may be mechanically movable to each cell culture vessel in the same or similar manner as a microscope may be moved to image each cell culture vessel. In embodiments, an LED and light sensor may be mechanically movable to each cell culture vessel in the same or similar manner as a microscope may be moved to monitor the color of the cell culture vessel.

[0074] In some exemplary implementations, one or more off-tray devices can be interfaced with an automated cell culture system. For example, an automated cell counter machine can be fluidly connected to a selectable port of a multiport valve so that a sample of the contents of the cell culture vessel can be transported to the automated cell counter machine. In some embodiments, the automated cell counter machine can be controlled by a controller so that the entire process of counting cells with the automated cell counter machine is automated by the automated cell culture system. As a further example, a cell counting chamber can be fluidly connected to a selectable port of a multiport valve so that a sample of the contents of the cell culture vessel can be transported to the cell counting chamber. A microscope can image the cell counting chamber and count the cells in the cell counting chamber. As a further example, an outer chamber can be fluidly connected to a selectable port of a multiport valve so that a sample of the contents of the cell culture vessel can be transported to the outer chamber. An LED and a light sensor can be used to measure the cloudiness of the solution in the outer chamber. As a further example, to collect a sample of cells, a sampling device can be sterilely connected to a port of a multiport valve, a sample of the contents of a cell culture vessel can be transferred to the vessel, and the vessel can then be sterilely cut and the cells collected.

[0075] Some operations of an automated cell culture system may require various support methods or procedures. For example, a fluid line or pump may need to be primed before pumping fluid through the line. As an example, a fluid line from a bottle of new growth medium to a multiport valve may need to be primed before pumping new growth medium into the cell culture vessel. To do this, a small amount of new growth medium can be pumped from the new growth medium bottle to a waste bottle, making sure there are no air pockets in the line.

[0076] Similarly, lines, pumps, or valves may need to be periodically cleaned or flushed to remove contaminants. This can be accomplished by pumping a cleaning solution through the lines, pumps, or valves for a period of time, or until the lines, pumps, or valves are sufficiently flushed.

[0077] 11 shows steps of a method for maintaining adherent cell lines. In step 1101, spent cell culture growth medium in a vessel is pumped from the vessel to a waste container. In step 1102, a determined amount of fresh cell culture growth medium is pumped into the vessel.

[0078] Figure 12 shows steps of a method for maintaining or expanding an adherent cell line with passaging to a new cell culture vessel. In contrast to the method discussed in connection with Figure 11, here, adherent cells in a cell culture vessel are transferred to a new vessel. In step 1201, cell culture growth medium in the vessel is pumped from the vessel to a waste container. Next, in step 1202, a wash solution is pumped into the vessel, and the vessel can optionally be agitated in step 1203. Next, the wash solution is pumped from the vessel to a waste container in step 1204.

[0079] In step 1205, a dissociation reagent is pumped into the vessel. An example of a dissociation reagent is trypsin. The dissociation reagent is used to resuspend cells adhered to the walls of the cell culture vessel. Depending on the cells being cultured and the dissociation reagent used, the cell culture vessel may be gently agitated to help detach the adherent cells from the walls of the cell culture vessel. The automated cell culture system then waits in step 1206 for a configurable period of time, depending on the cells being cultured and the dissociation reagent used. In an alternative embodiment, the automated cell culture system dynamically monitors the dissociation of the cells from the vessel with a microscope to determine when the amount of dissociation reaches a threshold. The vessel may optionally be agitated while waiting in step 1206. In step 1207, the cells are optionally imaged to observe the detachment of the adherent cells. If the cells are not sufficiently detached, the automated cell culture system may wait an additional period of time. Once the adherent cells have been sufficiently detached from the walls of the cell culture vessel, a dissociation reagent inhibitor or neutralizer may be pumped into the cell culture vessel to stop the action of the dissociation reagent. In step 1208, the contents of the cell culture vessel may optionally be removed from the automated cell culture system and spun inside a centrifuge to separate the cells from the liquid contents of the cell culture vessel and then resuspended. In step 1209, the cells may be counted to determine the total number of cells or cell density and viability. In step 1210, a portion of the cells are transferred to a new cell culture vessel. Then, in step 1211, a determined amount of new growth medium is pumped into the new vessel. If the automated cell culture system is configured only to maintain a cell line, the original cell culture vessel may be removed from the system and discarded, with only the new vessel remaining in the system for cell expansion. If the automated cell culture system is configured for cell line expansion, the original vessel may be retained and a proportional amount of new growth medium may be added to it, such that both the original and new cell culture vessels remain in the system for cell expansion. Although described in the context of using a single new vessel, it should be understood that this process can be extended to any number of vessels, such that a single original vessel can be divided into any number of new vessels.

[0080] FIG. 13 shows steps of a method for maintaining suspension cell lines with optional passaging. In step 1301, the cell culture vessel can be gently agitated to evenly distribute the cells within the growth medium in the vessel. Next, in step 1302, the cells in the vessel are counted, and in step 1303, an optimal amount of new growth medium is determined based on the cell number or cell density. In step 1304, the final liquid volume of the cell culture vessel after adding the determined amount of new growth medium is determined. Each time a procedure adds liquid to the cell culture vessel, the amount of liquid added is recorded and tallied by the controller. In this way, the controller maintains a current value of the amount of liquid in each cell culture vessel. In step 1305, the estimated final fluid volume of the cell culture vessel is compared to the maximum volume configured for the particular cell culture vessel being used. For example, the total volume of the vessel cannot exceed the total capacity of the vessel. In some embodiments, the threshold maximum volume may be significantly less than the total volume of the vessel. If the estimated final fluid volume is lower than the configured threshold, then in step 1306, a determined amount of new medium is added to the vessel. If the estimated final fluid volume is greater than the configured threshold, then the automated cell culture system can divide the contents of the cell culture vessel into two or more cell culture vessels to accommodate the estimated final fluid volume. In this exemplary method, the contents of the cell culture vessel, now referred to as the first cell culture vessel, are divided between the first cell culture vessel and an additional second cell culture vessel. In step 1307, a portion of the contents of the first cell culture vessel can be transferred to the second cell culture vessel. The ratio of the contents of the first and second cell culture vessels is recorded by the controller. Next, in step 1308, a proportional amount of new cell culture growth medium is added to each of the first and second cell culture vessels in proportion to the amount of final liquid volume each contains. For example, if the fluid contents of a first cell culture vessel are divided evenly between the first cell culture vessel and a second cell culture vessel, the fresh medium will likewise be divided equally between the first and second cell culture vessels.

[0081] 14 illustrates steps of a method for expanding suspension cell lines. The method for expanding suspension cell lines mirrors the method for maintaining suspension cell lines, except that in step 1407, the contents of the vessel can be transferred to a new cell culture vessel even if the total volume remains below the total volume threshold of the cell culture vessel. That is, cells can be transferred to a new cell culture vessel when appropriate to promote cell growth, rather than just in response to a lack of volume in the cell culture vessel.

[0082] 15 illustrates an exemplary machine of a computer system upon which a set of instructions for causing the machine to perform any one or more of the methodologies discussed herein may be executed. In alternative implementations, the machine may be connected (e.g., networked) to other machines in a LAN, an intranet, an extranet, and / or the Internet. The machine may operate in the capacity of a server or a client machine in a client / server network environment, as a peer machine in a peer-to-peer (or distributed) network environment, or as a server or client machine in a cloud computing infrastructure or environment.

[0083] The machine may be a personal computer (PC), tablet PC, set-top box (STB), personal digital assistant (PDA), mobile phone, web appliance, server, network router, switch, or bridge, or any machine capable of executing a set of instructions (sequential or otherwise) that specify actions to be performed by that machine. Moreover, although a single machine is depicted, the term "machine" should also be taken to include any collection of machines that individually or jointly execute a set (or sets) of instructions to perform any one or more of the methodologies discussed herein.

[0084] The exemplary computer system 1500 includes a processing device 1502, a main memory 1504 (e.g., read-only memory (ROM), flash memory, dynamic random access memory (DRAM), such as synchronous DRAM (SDRAM) or Rambus DRAM (RDRAM)), a static memory 1506 (e.g., flash memory, static random access memory (SRAM)), and a data storage device 1518, which communicate with each other via a bus 1530.

[0085] Processing device 1502 represents one or more general-purpose processing devices, such as a microprocessor, a central processing device, etc. More specifically, the processing device may be a complex instruction set computing (CISC) microprocessor, a reduced instruction set computing (RISC) microprocessor, a very long instruction word (VLIW) microprocessor, or a processor implementing other instruction sets or a processor implementing a combination of instruction sets. Processing device 1502 may also be one or more special-purpose processing devices, such as an application-specific integrated circuit (ASIC), a field-programmable gate array (FPGA), a digital signal processor (DSP), a network processor, etc. Processing device 1502 is configured to execute instructions 1526 to perform the operations and steps discussed herein.

[0086] Computer system 1500 may further include a network interface device 1508 for communicating over a network 1520. Computer system 1500 may also include a video display unit 1510 (e.g., a liquid crystal display (LDC) or a cathode ray tube (CRT)), an alphanumeric input device 1512 (e.g., a keyboard), a cursor control device 1515 (e.g., a mouse), a graphics processing unit 1522, a signal generation device 1516 (e.g., a speaker), a graphics processing unit 1522, a video processing unit 1528, and an audio processing unit 1532.

[0087] The data storage device 1518 may include a machine-readable storage medium 1524 (also known as a computer-readable medium) on which one or more sets of instructions or software 1526 embodying any one or more of the methodologies or functions described herein are stored. The instructions 1526 may also reside, completely or at least partially, within the main memory 1504 and / or within the processing device 1502 during execution thereof by the computer system 1500, with the main memory 1504 and the processing device 1502 also constituting machine-readable storage media.

[0088] In one embodiment, instructions 1526 include instructions for performing functions corresponding to components of a device for executing the disclosure herein. While machine-readable storage medium 1524 is shown to be a single medium in the exemplary implementation, the term "machine-readable storage medium" should be understood to include a single medium or multiple media (e.g., a centralized or distributed database and / or associated caches and servers) that store one or more sets of instructions. The term "machine-readable storage medium" should also be understood to include any medium that can store or encode a set of instructions for execution by a machine, causing the machine to perform any one or more of the methodologies of the present disclosure. Thus, the term "machine-readable storage medium" should be understood to include, but is not limited to, solid-state memory, optical media, and magnetic media.

[0089] 16A-16C show schematic diagrams of an automated cell culture system according to another embodiment. This exemplary automated cell culture system 1600 includes a consumable or disposable cell culture tray assembly 1601 (also referred to herein as a "tray assembly"; see FIG. 16A) and a reusable base unit 1620 (see FIG. 16B). The disposable tray assembly 1601 includes various components, described below, some of which are pre-assembled on (or together with) the tray assembly 1601 and enclosed within a protective overwrap to maintain the components in a sterile state. Some of the components of the tray assembly 1601 can be added to the tray assembly 1601 in a sterile environment (e.g., a laminar flow hood) before using the tray assembly 1601 in a cell culture procedure. Once the tray assembly 1601 is assembled and ready for use, the tray assembly 1601 can be coupled to the base unit 1620, as described in more detail herein.

[0090] As shown in FIG. 16A , tray assembly 1601 includes a tray 1602 that can be removably coupled to a base unit 1620, as described herein. In some embodiments, tray 1602 can include one or more transparent or cutout portions such that objects placed on an upper surface of tray 1602 can be viewed from below tray 1602. For example, as described in more detail below, cell culture system 1600 can optionally include imaging devices and / or other sensors disposed in base unit 1620 and below tray 1602 when tray assembly 1601 is coupled to base unit 1620. The transparent portion(s) or cutout(s) can allow images and / or other data to be acquired through the transparent portion or cutout, such as of the contents of a cell culture vessel coupled to tray 1602, as described in more detail below. In some embodiments, tray assembly 1601 can include a cell counting chip 1617, as shown in FIG. 16A . The cell counting chip 1617 can also include a bottom transparent portion, which can be used to obtain information about the contents of the cell culture vessel, as described below. In some embodiments, the cell counting chip 1617 can be coupled to or mounted within the base unit 1620 instead of being pre-assembled on the tray assembly 1601.

[0091] The tray assembly 1601 also includes one or more couplers 1603 that can be used to hold a cell culture vessel or container. The tray 1602 can optionally include holders 1604 that can be used to removably couple reagent containers 1605 and waste containers 1606 to the tray 1602 (e.g., to secure the containers during transport, initial setup, etc.). While two couplers 1603 are shown, in other embodiments, only one or more of the two couplers 1603 can be present. For example, in some embodiments, the tray assembly can be configured to support only one cell culture vessel and thus includes only a single coupler 1603 that maintains the cell culture vessel in a fixed position on the tray. Similarly, while only one waste container 1606 and only one reagent container 1605 are shown, in alternative embodiments, multiple waste and multiple reagent containers can be present. 16A shows the waste container 1606 and the reagent containers 1605 as part of the tray assembly 1601, in other embodiments, the waste container 1606 and / or the reagent containers 1605 can be separate components within the automated cell culture system 1600 that are not coupled to the tray 1602 during use. For example, in some embodiments, the reagent containers 1605 can be used to contain cell culture media and can be located in a refrigerated portion (not shown) of the automated cell culture system 1600 or in a separate refrigerated location. The coupler 1603 and the holder 1604 can be separate components attached to the tray 1602 or can be components integral with or monolithically formed with the tray 1602. For example, in some embodiments, the coupler 1603 and / or the holder can include a deformable bracket, a movable pin, or any other suitable structure for coupling the container to the tray 1602. In some embodiments, the tray assembly 1602 may optionally include a handle 1614 that may be used by a user to move and carry the tray assembly 1602. The handle 1614 may be a separate component from the tray 1602, or may be integrally or monolithically formed with the tray 1602.In some embodiments, tray assembly 1601 may not include holder 1604. In some embodiments, not shown, tray assembly 1601 may be pre-assembled with one or more cell culture vessels.

[0092] The tray assembly 1601 also includes a multiport valve 1607 and one or more container lids 1608 (FIG. 16A shows two container lids 1608). The container lids 1608 can be coupled to the tray 1602 using disposable packaging mounts (not shown in FIGS. 16A-16C). Each of the lids 1608 is configured to couple to a different cell culture vessel, as described below. In this illustrative embodiment, there are two lids 1608, but it should be understood that a different number of lids 1608 can be provided to accommodate a different number of cell culture vessels. Each of the lids 1608 can include a liquid exchange port (also referred to herein as a "fluid port") and a gas exchange port (each not shown in FIGS. 16A-16C). As shown, each of the fluid ports is coupled to a selected port of the multiport valve 1607 with tubing (see tubing A, B, C, and D in FIG. 16A). The gas exchange port can allow for the transfer of gas from the cell culture vessel to which it is coupled. For example, in some embodiments, lid 1608 can be similar to lid 803 or lid 2408 of the cell culture vessel shown and described herein. For example, lid 1608 can include a gas filter that prevents microorganisms and / or contaminants from entering the cell culture vessel, thereby allowing cell culture and fluid transfer through lid 1608 while maintaining a closed (and / or sterile) system with other vessels in the system (e.g., reagent vessels 1605, waste vessel 1606, or other vessels). In some embodiments, the tray assembly can optionally include lids 1609 and 1610 coupled to reagent vessels 1603 and waste vessel 1606, respectively. Lid 1609 and / or lid 1610 can be similar in structure and function to lid 1608 and / or cell culture vessel lid 803.

[0093] Multiport valve 1607 can include the same or similar components and functionality in the same or similar manner as the multiport valves described above for previous embodiments (e.g., multiport valve 600 or multiport valve 2407 described herein). Multiport valve 1607 can include a master port (described below and shown in FIGS. 16B and 16C ) configured to couple to a fluid pump 1613 of a base unit, and multiple selectable ports that can be fluidly coupled to liquid exchange ports of lids 1608, 1609, 1610, and / or other components of cell culture assembly 1600, as described herein. For example, one port of the selectable ports can be sterilely and / or fluidly coupled to a first liquid exchange port of a first lid 1608, and a second selectable port can be sterilely and / or fluidly coupled to a second liquid exchange port of a second lid 1608. In some embodiments, the third port of the multiport valve 1607 can be coupled to a liquid exchange port of a reagent container 1605, the fourth port can be coupled to a liquid exchange port of a waste container 1606, and the fifth port can be coupled to a liquid exchange port of a cell collection container (not shown in FIGS. 16A-16C ). The multiport valve 1607 can be coupled to various other components, such as, for example, a cell counting chip, cell collection container(s), various reagent and enzyme containers, etc. A schematic diagram of an exemplary system showing some exemplary connections of the multiport valve is presented in FIG. 59 . Thus, when actuated, the multiport valve 1607 can facilitate the exchange of fluids between various containers within the automated cell culture system 1600. For example, as described herein, the multiport valve 1607 can be actuated to facilitate the addition of cell culture media or reagents to a cell culture container, the removal of cells from a cell culture container (e.g., cell passaging or cell harvesting), and any other fluid movement associated with culturing cells.

[0094] The multi-port valve 1607 can be pre-assembled and coupled to the lids 1608, 1609, 1610 on the tray assembly 1601 and enclosed within the protective overwrap 1615. This arrangement allows an end user to receive the tray assembly 1601 pre-packaged within the protective overwrap. In some embodiments, the tray assembly 1601 can be sterilized before being placed in the protective overwrap. As described herein, the user can then load the desired cells, reagents, cell culture media, etc. into the containers and couple the pre-connected lids to the containers in a sterile environment. The tray assembly 1601 can then be coupled to a base unit and moved to an incubation environment where fluid exchanges can be performed to ensure the culture of the desired cells, as described herein.

[0095] The multiport valve 1607 is configured to engage with a valve actuator 1621 of the base unit 1620. The multiport valve 1607, in some embodiments, can include a mounting portion 1616 configured to mate and couple with a valve connector 1622 of the base unit 1620. For example, the mounting portion 1616 can be shaped so that it can couple with the valve connector 1622 in a puzzle-like manner. Examples of such mounting portions and valve connectors are described below with reference to specific embodiments. As shown in FIGS. 16B and 16C , when the multiport valve 1607 is engaged with the valve actuator 1621 of the base unit 1620, the valve actuator 1621 actuates the multiport valve 1607 to move to a selected port, enabling selective fluid transfer of various vessels and cell culture vessels in the tray assembly 1601 (described below). In some embodiments, the multiport valve 1607 can be coupled to the valve actuator 1621 while coupled to the tray 1602. For example, a valve connector (not shown) coupled to a valve actuator 1621 can be located in the base unit 1620 below where the tray assembly 1602 is removably coupled to the base unit 1620 (e.g., similar to base unit 302 or base unit 2120 described herein). In some embodiments, the multiport valve 1607 can be removed from the tray 1602 (while remaining coupled to the lid, thereby maintaining a closed system) and attached to a mating valve connector 1622 on the base unit 1620, as shown, for example, in FIGS. 16B and 16C . FIG. 16B shows the connector 1622 without the multiport valve 1607 coupled thereto, and FIG. 16C shows the multiport valve 1607 coupled thereto. In other words, the multiport valve 1607 can be removed from the mating mounting pocket 1618 (see FIG. 16C ) on the tray 1602 and attached to the valve connector 1622 on the base unit 1620.As described above, the mounting portion 1616 of the valve 1607 is shaped to matingly engage with the mounting pocket 1618 and the valve connector 1622 of the base unit 1620 to ensure proper positioning and alignment within both the tray assembly 1601 and the base unit 1620. This repositioning of the multiport valve 1607 can be performed while the lids 1608, 1609, 1610 remain sterilely coupled to the multiport valve 1607. Removing the valve 1607 from the tray 1602 allows the interface between the valve 1607 and the valve actuator 1621 to be fixed, which is well suited to embodiments including an agitator that moves the tray 1602 relative to the base unit 1620. Similarly, by directly coupling the valve 1607 to the base unit 1620, the interface between the valve 1607 and the valve actuator 1621 is not disturbed by relative movement between the tray 1601 and the base unit 1620.

[0096] Also shown in FIG. 16A is an optional pump holder 1611 that can be used to hold a port connector 1612 fluidly coupled to the master port of the multiport valve 1607. This port is used to connect a fluid pump 1613 to the tray fluidics 1602 during preparation of the tray assembly 1601 for cell culture procedures. The fluid pump 1613 can be used to generate fluid movement in the cell culture system 1600, as described herein. The fluid pump 1613 can be any suitable pump that generates pressure and / or flow within the cell culture system 1600. For example, the fluid pump 1613 can be a syringe including a piston rod and a syringe body. A syringe is but one example of a type of fluid pump that can be used in the cell culture system 1600. Various other positive displacement fluid pumps, such as peristaltic pumps, can be used. In some embodiments, the pump can be a single-port pump, while in other embodiments, the pump can be a two-port pump, as described herein. If a syringe is used as pump 1613, it can be attached to multiport valve 1607 and optional syringe holder 1611 in a sterile environment prior to the cell culture procedure.

[0097] The base unit 1620 (see FIGS. 16B and 16C ) includes a housing 1623 that supports various components of the base unit 1620 and can define (or include) a receiving portion 1624 that receives and removably couples the tray assembly 1601. In some embodiments, the receiving portion 1624 can include an opening into which the tray assembly 1601 can be positioned and supported by a tray support (not shown). In some embodiments, the tray assembly 1601 is supported by a support portion of the base unit 1620 such that the tray assembly 1601 is elevated above the top surface of the base unit 1620. In some embodiments, the tray assembly 1601 is at least partially supported by engagement with an agitator (described below) of the base unit 1620. In some embodiments, the tray assembly 1601 can be removably coupled to a separate support member that is connectable to the housing 1623 of the base unit 1620. The base unit 1620 may also include one or more transparent or opening portions corresponding to the transparent portions of the tray 1602 so as to be able to acquire images and / or other sensor data related to the contents of the cell culture container.

[0098] The base unit 1620 includes the valve connector 1622 and valve actuator 1621 described above, and also includes a fluid pump portion 1627 and a pump actuator 1626. The pump actuator 1626 can be at least partially disposed within an opening 1625 defined by the housing 1623, for example. As described above, in some embodiments, the fluid pump 1613 can be a syringe or other type of positive displacement fluid pump that is fluidly coupled to the multiport valve 1607, which in turn is coupled to the fluid pump portion 1627 of the base unit 1620. In some embodiments where a syringe is the fluid pump 1613, the fluid pump portion 1627 can include a holder (not shown in FIGS. 16A-16C ) that can be used to hold and support the syringe 1613 in the housing 1623. The holder can be a separate component or a component integral or monolithically formed with the housing 1623. The fluid pump 1613 can be fluidly coupled to a master port of the multiport valve 1607. In this exemplary embodiment, as shown in FIG. 16C (showing the tray assembly 1601 coupled to the base unit 1620), the multi-port valve 1607 is disconnected from the tray assembly 1601 and coupled to the valve connector 1622, and the fluid pump 1613 is coupled to the master port by tubing E. The fluid pump 1613 may include a movable member within the pump body (not shown in FIGS. 16B and 16C). During operation of the system 1600, the movable member (e.g., plunger, rotor) of the fluid pump 1613 can be actuated to create suction to move fluid into the pump body, and the movable member can be actuated to force the fluid out of the pump body, as described above for the previous embodiments.

[0099] In some embodiments, the base unit 1620 also includes an agitator 1628. The agitator 1628 can include, for example, an orbital shaker that moves the tray 1602 in a circular or semicircular motion. The agitator 1628 can be configured to agitate the removable tray assembly 1601 in relation to the housing 1623, as described above for previous embodiments. The agitator 1628 can agitate the tray 1602 with a rocking, vibrating motion, a circular orbital motion, or other motion useful for culturing cells. In some embodiments, individual cell incubators / vessels can be independently agitated by separate agitators positioned between the cell incubator and the removable tray assembly 1601, as described above. In some embodiments, an agitator may not be included.

[0100] In some embodiments, the base unit 1620 may also optionally include one or more sensors 1629 (only one shown in FIGS. 16B and 16C ) and an electronic control system 1630 for controlling the operation of any components of the cell culture system 1600 (e.g., valve actuators 1621, pump actuators 1626). The electronic control system 1630 may optionally be incorporated within, coupled to, or provided by a remote computing system, such as, for example, in a cloud computing environment. In some embodiments, the sensor(s) 1629 may be attached to the device to allow the sensor(s) to be movable relative to the housing 1623 of the base unit 1620. Examples of such embodiments are described below with reference to FIGS. 32-34 . The sensor 1629 may include, for example, one or more imaging devices, microscopes, color monitors, or any other type of sensor described herein. The sensor(s) can be used to obtain images or other types of output that can be used to determine information about the contents within the cell culture vessel (e.g., 1647, 1648), such as the density of the contents to determine the amount of cells inside the vessel during a cell culture procedure (e.g., for suspension cells), or the percentage of confluence (i.e., the coverage of the vessel's area by cells) for adherent cells, for example. In some embodiments, the sensor(s) 1629 can be used to capture images and / or other types of output of a sample portion of the contents of the cell culture vessel via the cell counting chip 1617. For example, a sample of the fluid mixture within the cell culture vessel can be extracted into the cell counting chip 1617, and the sensor 1629 can be moved into alignment with the cell counting chip 1617 and used to image or otherwise collect information related to the sample fluid mixture on the cell counting chip 1617. In some embodiments, the sensor(s) 1629 may be operably coupled to or incorporated within the electronic control system 1630 .

[0101] As noted above, in some embodiments, a light or light source 1682 (see FIGS. 16B and 16C) can also be provided that can be used in combination with, for example, an imaging device. In some embodiments, the light can be movable relative to the housing of the base unit 1620. For example, the light source can be mounted above the tray assembly 1601 of the system on a movable multi-axis gantry, which can be controlled to move to the same position as the microscope within the base unit. In some embodiments, the light source can be operably coupled to the same gantry as the imaging device such that the imaging device and light source can be moved together. In some embodiments, the system 1600 can include one or more cameras or LED and light sensor pairs to image the contents of the cell culture vessel.

[0102] In some embodiments, the sensor(s) 1629 can include a valve position sensor configured to generate a valve position signal related to the rotational position of the valve actuator. In this manner, the valve position sensor can detect which of the selectable ports is fluidly coupled to the master port (e.g., fluid pump 1613). In some embodiments, the sensor(s) 1629 can include a pump position sensor configured to generate a pump position signal related to pump movement. In this manner, the pump position sensor can indicate pump movement and / or the volume of fluid moved by the pump. As described herein, the electronic control system 1630 can determine an estimated amount of fluid in (or added to) one of the cell culture vessels based on the pump position signal.

[0103] Figure 17 is a schematic diagram of an electronic control system 1630 that can be used to control the operation of a cell culture system. The components and architecture of electronic control system 1630 are provided as an example, and in some embodiments, electronic control system 1630 (or any of the electronic control systems described herein) can include different components than those shown in Figure 17. Furthermore, in some embodiments, the base unit and / or cell culture assembly need not include an electronic control system as described in Figure 17. For example, in some embodiments, base unit 1620 (or any of the base units described herein) can include computer system 1500 as described herein. In other embodiments, base unit 1620 need not include an electronic control system.

[0104] 17 , the electronic control system 1630 includes one or more processors 1631, one or more memory components 1632, a radio 1633, and various modules, such as an actuation module 1634, an agitation module 1635, a fluid flow module 1636, a valve module 1637, a pump module 1638, a measurement module 1641 (also referred to as a cell sensor module), and / or a network module 1640. While FIG. 17 illustrates the electronic control system 1630 within the base unit 1620, as described above, the electronic control system 1630, or portions thereof, can be provided outside the base unit 1620 (e.g., in a cloud computing environment). The electronic control system 1630 can automatically control the flow of fluids into and out of various vessels, for example, through the operation of pump actuators 1626 and valve actuators 1621. The electronic control system 1630 can also automatically control the operation of an agitator 1628, sensor(s) 1629, and valve actuators 1621. The operation and actuation of the fluid pump 1613, valve actuator 1621, selection of ports on the multiport valve 1607, etc. can be the same as or similar to the operation of these components as described above for the previous embodiment. In operation, the combination of the fluid pump, valves of the multiport valve, vessel, and cell incubator can be used to transfer fluids between the cell incubator and vessel, as described above for the previous embodiment.

[0105] In preparation for a cell culture procedure, the tray assembly 1601 can be placed in a sterile environment (e.g., a laminar flow hood) and the overwrap 1615 can be removed. While in the sterile environment (e.g., a flow hood), the cell culture vessels or containers 1617, 1618 can be prepared (e.g., cells and reagents can be added to the containers), secured to the lids 1608, and placed within the couplers 1603 on the tray 1602. The cell culture vessels 1617, 1618 can be any known type of cell culture vessel, such as, for example, the flasks or dishes described above for previous embodiments. The waste container 1606 and the reagent containers 1605 can be placed in an upright position within the holder 1604. In other embodiments, the waste container 1606 and / or the reagent containers 1605 can be placed in any suitable location for transport elsewhere within the cell culture system 1600.

[0106] The tray assembly 1601 can then be coupled to the base unit 1620, as shown in FIG. 16C. In this embodiment, the multiport valve 1607 is decoupled from the tray assembly 1601 and matingly coupled to the valve actuator 1621, while remaining fluidly coupled to the various lids 1608, 1609, 1610. The fluid pump 1613 can be fluidly coupled to the multiport valve 1607 via a length of tubing E. As noted above, in the case of a syringe used as the fluid pump 1613, the syringe can be coupled to the multiport valve 1607 inside a sterile environment and may be coupled to the tray 1602 before the tray assembly 1601 is coupled to the base unit 1620. The syringe 1613 can then be moved to a holder (not shown) in the base unit 1620 and coupled to the pump actuator 1626, while remaining fluidly coupled to the multiport valve 1607 via tubing. The waste container 1606 and reagent containers 1605 may be removed from the tray 1602 and placed, for example, along or near the tray 1602 and / or in an incubator or refrigerator. A more detailed description of how to prepare the cell culture system 1600 for use is described below with reference to FIGS. 21-30. The tray assembly 1601 can be coupled to a base unit 1620 inside a sterile environment or outside a sterile environment. The cell culture system (with the tray assembly 1601 coupled to the base unit 1620) can be placed in an incubator ready for cell culture treatment. In some embodiments, the tray assembly 1601 can be coupled to the base unit 1620 inside the incubator.

[0107] Any of the base units and / or tray assemblies described herein can be used to perform any of the computer-implemented methods described herein. Stated another way, any of the base units and / or tray assemblies described herein can include (or interface with) an electronic control system to facilitate an automated (or semi-automated) method of culturing cells. As shown in FIG. 17 , electronic computer system 1630 can communicate with other remote computing devices (e.g., computing device 1643) via a network 1646 (e.g., the Internet), for example, via a service platform 1642 and a cell culture application (i.e., app) 1644. Electronic control system 1630 can communicate with remote computing devices in addition to, or instead of, a remote computing device via a direct connection, such as a cable connected to a USB port on base unit 1620. The components, modules, and / or functionality described in connection with cell culture system 1600 can be included in any of the cell culture systems described herein. For example, although not shown, cell culture systems 200, 300, and 400 can include an electronic control system similar to or the same as electronic control system 1630. Additionally, although cell culture system 1600 is shown and described as including only one connected computing device 1643, in other embodiments, cell culture system 1600 (and any of the cell culture systems described herein) can include any of any number of connected remote computing devices.

[0108] The service platform 1642, which can be any suitable computer-implemented interface and / or computing entity, such as a server or personal computer, is configured to communicate with a remote computing device 1643 and / or any other portion of the cell culture system 1600 (e.g., a call center interface, other remote computing devices, etc., not shown) via a network 1646. More specifically, the service platform 1642 can receive information from devices within the cell culture system 1600 (e.g., the base unit or the remote computing device), manipulate the information, and generate information for any other device within the cell culture system 1600. For example, in some embodiments, cell density or cell confluence information associated with the tray assembly 1601 can be transmitted from the base unit 1620 to the remote computing device 1643. The remote computing device 1643 can generate notifications to a user via the cell culture application 1644 and can receive input from the user in response to such notifications. The remote computing device 1643 can then transmit the input (or instructions) to the service platform 1642. Based on user input, service platform 1642 can send instructions to base unit 1620, which can then execute the instructions to perform the desired task (e.g., passaging the cells). In this manner, service platform 1642 can control and / or manage certain commands, notifications, and / or functions. Also mentioned, in this manner, service platform 1642 can function as a "backend" for cell culture system 1600.

[0109] The network 1646 may be a piconet, the Internet, an intranet, a local area network (LAN), a wide area network (WAN), a virtual network, a telecommunications system, any other suitable communications system, and / or a combination of such networks. The network 1646 may be implemented as a wired and / or wireless network. The base unit 1620 and the remote computing devices 1643 may be coupled (or connected) to the network via any suitable mechanism and / or by any suitable protocol. For example, in some embodiments, the base unit 1620 may communicate directly with the network 1646, the remote computing devices 1643, and / or the service platform 1642 via the LTE Direct protocol or any other suitable protocol (e.g., a 5G mobile wireless standard based on the IEEE 802.11ac standard for broadband technology).

[0110] 17 identifies a base unit 1620, the electronic control system 1630 can be incorporated into (or used with) any of the base units described herein. As noted above, the base unit 1620 includes or has attached thereto the electronic control system 1630. For example, in some embodiments, the electronic control system 1630 can be coupled to and / or within the housing 1623 and / or any other portion of the base unit 1620. As also noted, the electronic control system 1630 can be incorporated within the base unit 1620. However, in other embodiments, the electronic control system 1630 can be separate from but operably coupled to (e.g., wirelessly connected or connected via a wired connection) the base unit 1620. Although the electronic control system 1630 is shown as including one or more processors 1631, one or more memory components 1632, a radio 1633, and various modules, such as an actuation module 1634, an agitation module 1635, a fluid flow module 1636, a valve module 1637, a pump module 1638, a measurement module 1641, and / or a network module 1640, in other embodiments, the electronic circuit system need not include all (or any) of these modules, but may include any other module described herein. For example, in some embodiments, the electronic control system may include only a flow module and be configured to perform its associated cell passaging and flow method, and need not include, for example, an agitation module.

[0111] Processor 1631, and any of the processors described herein, may be any suitable processor for performing the methods described herein. In some embodiments, processor 1631 may be configured to execute and / or process application modules, processes, and / or functions associated with cell culture system 1600. For example, processor 1631 may be configured to execute and / or process actuation module 1634, agitation module 1635, and / or network module 1640, and / or any of the other modules described herein, and to perform methods associated therewith. Processor 1631 may be, for example, a field programmable gate array (FPGA), an application specific integrated circuit (ASIC), a digital signal processor (DSP), etc. Processor 1631 may be configured to retrieve data from and / or write data to a memory, for example, memory 1632. As described herein, in some embodiments, processor 1631 may function in cooperation with radio 1633 and / or execute instructions from code to provide signals that communicatively couple electronic control system 1630 to computing device 1643 (e.g., via wireless communication) and / or any other computing entity over a network, such as network 1646. In some embodiments, processor 1631 is a Bluetooth Low Energy (BLE) processor.

[0112] The memory 1632 can be, for example, a random access memory (RAM), a memory buffer, a hard drive, a database, an erasable programmable read-only memory (EPROM), an electrically erasable programmable read-only memory (EEPROM), a read-only memory (ROM), flash memory, a hard disk, a floppy disk, cloud storage, etc. In some embodiments, the memory 1632 stores instructions that cause the processor 1631 to execute modules, processes, and / or functions associated with such cell culture system 1600 and / or base unit 1620. For example, the memory 1632 can store instructions that cause the processor 1631 to execute any of the application modules described herein and perform the associated methods.

[0113] As described above, the one or more sensor(s) 1629 can be separate and / or can be included within the electronic control system 1630 and can include, for example, imaging devices, optical sensors, accelerometers, temperature sensors, contact sensors, position sensors, and / or any other suitable input devices. In some embodiments, the sensor(s) 1629 can include sensors operable to monitor and / or measure the position (or selection) of a port of the multiport valve 1607, the position of the fluid pump 1627, temperature, agitation, etc. For example, in some embodiments, the sensor 1629 can include a position sensor operable to detect the position of a multiport valve of the system. As yet another example, the sensor 1629 can include an optical sensor operable to detect the density (or amount) of cells in a cell culture vessel coupled to the tray 1602. In such an embodiment, the optical sensor can detect light attenuation (e.g., to detect the density of cells in the light path). Alternatively, the optical sensor can acquire an image (e.g., via a photocell, microscope, charge-coupled device, etc.) to determine the amount of cells in the cell culture vessel. As yet another example, the sensor 1629 may include an accelerometer operable to detect characteristic movement or vibration characteristics of the tray assembly 1601 when the device is being agitated.

[0114] Radio 1633 (also referred to as a receiver, transmitter, and / or transceiver) may be operable to transmit and / or receive signals over a wireless network, such as Bluetooth, ZigBee, Wi-Fi, etc., where 1631 is a Bluetooth processor and radio 1633 may be integrated with processor 1631. In other embodiments, radio 1633 may include a different processor than processor 1631. Radio 1633 may be operable to communicatively couple electronic control system 1630 to computing device 1643 and / or any other computing entity via network 1646. Radio 1633 may include or be coupled to a ceramic chip antenna, a stamped antenna, a sintered antenna, a PCB conductive trace antenna, and / or any other suitable antenna.

[0115] Measurement module 1641 (also referred to in some embodiments as a cytosensor module) can be a hardware and / or software module (stored in memory 1632 and / or executed on processor 1631). As described in more detail herein, in some embodiments, measurement module 1641 is configured to receive a number of different signals from sensors 1629 of electronic control system 1630 and generate information for various other modules within electronic control system 1630.

[0116] The flow module 1636 can be a hardware and / or software module (stored in memory 1632 and / or executed by the processor 1631). As described in more detail herein, the flow module 1636 can be configured to receive indications (e.g., from sensor(s) 1629) and / or transition information related to changes in the state of the multiport valves of the pump or base unit 1620, and based on the indication or transition information, determine which valves of the multiport valve 1607 to open or close to allow fluid to flow into or out of particular vessels of the system 1600.

[0117] The network module 1640 can be a hardware and / or software module (stored in memory 1632 and / or executed on the processor 1631). The network module 1640 is configured to exchange information related to the base unit 1620 and the remote computing device 1643 to facilitate the communication process. For example, the network module 1640 of the base unit 1620 can cause the remote computing device 1643 and the base unit 1620 to exchange short-term and / or long-term security keys to complete the pairing and bonding process.

[0118] The notification module 1639 can be a hardware and / or software module (stored in memory 1632 and / or executing on processor 1631). The notification module 1639 is configured to generate notifications related to any of the methods and / or application modules described herein. For example, in some embodiments, the notification module 1639 can generate notifications that are transmitted via radio 1633 and received by a notification module of a remote computing device 1643. In this manner, the notification module 1639 executing in the cell culture application can generate an output (e.g., a wireless communication signal, a GUI element, an audible output, a visual output, etc.) to notify a user of an event.

[0119] The agitation module 1635, the valve module 1637, and the pump module 1638 can each be hardware and / or software modules (stored in memory 1632 and / or executed by the processor 1631). These modules can be configured to receive indications (e.g., from sensor(s) 1629) and / or transition information related to changes in the state of a pump or multiport valve of the base unit 1620, and determine what action to perform on a particular device (e.g., a pump, valve, agitator, etc.) based on the indication or transition information. In some embodiments, the valve module 1637 and / or the pump module 1638 can provide information related to the position of the multiport valve 1607 and the pump 1627, respectively. In some embodiments, the modules 1637 and 1638 can include (or accept information from) an encoder. In some embodiments, the actuator module 1634 can perform some or all of the functions of the agitation module 1635, the valve module 1637, and / or the pump module 1638.

[0120] Computing device 1643 (or other "remote" computing device, such as a mobile computing entity, such as a smart mobile phone (e.g., an iPhone®, an Android® device, a Windows® phone, a Blackberry® phone, etc.), a tablet computer (e.g., an Apple iPad®, a Samsung Nexus® device, a Microsoft Surface® device, etc.), or a computer (e.g., a laptop, desktop, smart TV, etc.), and / or any other suitable computing entity. Computing device 1643 may include a processor, memory, a user interface 1645, and a radio.

[0121] The user interface 1645 of the remote computing device 1643 can be, for example, a monitor or screen that displays visual elements to a user. The user interface 1645 can be a touchscreen (such as a smart phone) that can display a series of graphical user interface (GUI) elements (e.g., windows, icons, input prompts, graphical buttons, data displays, notifications, etc.). In some embodiments, the graphical user interface elements (see, for example, GUI elements 1645A, 1645B, and 1645C described with reference to FIGS. 18-20 ) are generated by the cell culture application 1644. Additionally, the user interface can also receive input from a user, such as, for example, input via the touchscreen, input via a microphone, etc.

[0122] The cell culture application 1644 (also referred to as an "application" or "cell culture app") is configured to communicate with the electronic control system. In some embodiments, the application 1644 can communicate directly with the electronic control system 1630 located on the base unit 1620. In some embodiments, the application 1644 can communicate with the electronic control system 1630 via a computing cloud environment. The application 1644 can be used to set up, execute, and monitor various steps of a cell culture procedure using the cell culture system 1600. For example, the application 1644 can be used to cause the remote computing device 1643 to generate a series of prompts and information (e.g., via a user interface) to facilitate the cell culture methods described herein. Specifically, the cell culture application 1644 can cause the remote computing device 1643 to generate graphical user interface (GUI) elements that can include prompts for inputting various data for the cell culture procedure. FIGS. 18-20 are sample screenshots illustrating various GUI elements that can be generated by the remote computing device.

[0123] 21-30 illustrate a method of preparing a cell culture system for use in a cell culture procedure. Cell culture system 1700 shown in FIGS. 21-30 can include the same or similar components as other embodiments described herein (e.g., cell culture system 1600 or cell culture system 2000), and therefore, some details of cell culture system 1700 are not described with respect to this embodiment.

[0124] Cell culture system 1700 (also referred to herein as "system") includes tray assembly 1701 and base unit 1720 (see FIGS. 27-30). For example, as shown in FIG. 21, tray assembly 1701 includes tray 1702 in which the same or similar components are arranged as described above for other embodiments (e.g., tray assembly 1601 or tray assembly 2001). For example, tray assembly 1701 includes waste container 1706 coupled to lid 1710, reagent container 1705 coupled to lid 1709, and three lids 1708 (shown in FIGS. 25-27), each configured to couple to a cell culture container. Lids 1708, 1709, and 1710 can include liquid exchange ports (also referred to as "fluid ports") and gas exchange ports, as described above for the previous embodiments. Tray assembly 1701 also includes a multiport valve 1707 with a master port and multiple selectable ports, to which lids 1708, 1709, and 1710 can be selectively connected via lengths of tubing. Waste container 1706 and reagent containers are shown connected horizontally at holders 1704. Tray assembly 1701 also includes couplers 1703 to which cell culture vessels can be connected, as described below. Beneath where the cell culture vessels are placed is a transparent portion (or opening / cutout portion) 1758 of tray 1702. In this embodiment, syringe holder 1711 is provided to hold syringe port 1712. Syringe port 1712 is also connected to multiport valve 1707 using tubing T. FIG. 22 shows tray assembly 1701 encased within overwrap 1715 to maintain sterility of tray assembly 1701 during transport and storage. This arrangement allows the tray assemblies 1701 to be assembled at a central facility, placed in the protective overwrap 1715, and sterilized. Sterilization can be performed by any suitable method, including radiation sterilization, ethylene oxide (EtO) sterilization, or e-beam sterilization. The pre-packaged, sterilized tray assemblies 1701 can then be stored until needed for a cell culture procedure.

[0125] The first step in preparing a cell culture procedure is to prepare the cells and media (e.g., reagents) and prepare tray assembly 1701, which will be performed inside a sterile environment (e.g., a laminar flow hood). The cells and media are placed inside a cell culture vessel or vessels; in this example, there are positions for three cell culture vessels (e.g., 1747, 1748, and 1749 shown in Figures 26-27). Tray assembly 1701 is placed in a sterile environment (e.g., a hood) and overwrap 1715 is removed. Waste container 1706 and reagent container 1705 can be moved vertically within holder 1704 with lids 1709 and 1710 upright, as shown in Figure 23. In this example, fluid pump 1713 is a syringe, which can be removed from the outer sterile wrap, and port 1712 can then be connected to fluid pump 1713, as shown in Figure 23. 24. In some embodiments, the fluid pump 1713 (e.g., a syringe) is not included in the pre-packaged tray assembly 1701, but rather is a separate component. In other embodiments, the fluid pump 1713 (e.g., a syringe) is included in the pre-packaged tray assembly 1701.

[0126] After loading the cell culture vessels with cells and an initial amount of cell culture medium, lids 1708 are secured to cell culture vessels 1747, 1748, and 1749 with the cells and medium therein. Lids 1708 are first removed from transport supports 1795 (see FIG. 24 ) to which they are coupled. Transport supports 1795 are sized and configured to be received within lids 1708 to secure lids 1708 during transport, storage, and initial setup. This arrangement reduces the chance of unwanted movement and contamination of the interior of the lid during initial setup. Lids 1708 are then coupled to their respective vessels, while remaining fluidly connected to multiport valve 1707. Vessels 1747, 1748, and 1749 are coupled to couplers 1703 such that the vessels are positioned horizontally as shown in FIG. 25 . In this state, the bottom surfaces of cell culture vessels 1747, 1748, 1749 are aligned with transparent portion 1758 of the tray.

[0127] With the tray assembly 1701 fully assembled, as shown in FIG. 26, it can be placed onto the base unit 1720, as shown in FIG. 27. This can be done outside of a sterile environment because the components (e.g., container, lid, valve, syringe) are fluidly connected in a closed system. The tray assembly 1701 should be oriented so that the arrow (labeled and circled) on the tray 1702 points toward the base unit 1720, as shown in FIG. 27. As also shown in FIG. 27, the base unit 1720 includes a pump actuator 1726, a valve connector 1721, and a valve actuator 1722. In this embodiment, the multiport valve 1707 is removable from the tray 1702 and can be coupled to the base unit 1720. More specifically, the mounting portion 1716 of the multiport valve 1707 can be removed from the tray 1702 by removing the fasteners 1757 and attaching the mounting portion 1716 to a mating valve connector 1722 of the base unit 1720 with the same or different fasteners 1757, as shown in FIGS. 28 and 29. The fluid pump 1713 (e.g., a syringe) is disconnected from the tray assembly 1701 and coupled to a holder 1719 of the base unit 1720, as shown in FIG. 29. This operation is performed while the fluid pump 1713 remains fluidly coupled to the multiport valve 1707, thereby maintaining a closed system. The holder 1719 can be part of the fluid pump portion (e.g., 1627) of the base unit 1720, as described above for system 1600. As shown in FIG. 30, waste container 1706 and reagent containers 1705 can be removed from tray 1702 and placed near base unit 1720 (or any other suitable location).

[0128] The base unit 1720 and tray assembly 1701 can then be moved to an incubation environment (e.g., an incubator 2275 as shown in FIG. 58) to promote cell growth in a temperature-controlled environment when the tray assembly 1701 is coupled to the base unit 1720 outside the incubator. In some embodiments, the base unit 1720 is placed within the incubator when the tray assembly 1701 is coupled to it.

[0129] FIG. 31 is a flow chart illustrating a method 1850 of preparing a cell culture system for use in a cell culture procedure. Method 1850 can be performed using any of the cell culture systems described herein, such as cell culture system 1700 described above with reference to FIGS. 23-30. At 1851, a cell culture tray assembly is removed from its outer protective wrap. The tray assembly can be any of the tray assemblies described herein and includes a tray, a first lid, a second lid, and a multi-port valve. The first lid is coupled to the tray and configured to be removably coupled to a first container, and the second lid is coupled to the tray and configured to be removably coupled to a second container. The multi-port valve is coupled to the tray and includes a master port and multiple selectable ports. The first selectable port is aseptically coupled to a first liquid exchange port of the first lid, and the second selectable port is aseptically coupled to a second liquid exchange port of the second lid. As described herein, pre-coupling lids to appropriate ports reduces the number of operations performed during initial setup, thereby reducing the chance of contamination and error. At 1852, at least one cell sample is added to a first container through an opening in the first container, and at 1853, a volume of reagent (e.g., cell culture medium) is added to the first container through an opening in the first container. At 1854, a first lid is coupled to the first container to close the opening. In some embodiments, a second lid can optionally be coupled to a second container. At 1855, the tray assembly is coupled to a base unit. In some embodiments, when the tray assembly is coupled to the base unit, a valve actuator on the base unit simultaneously engages a multiport valve on the tray assembly. In some embodiments, a valve actuator engages the multiport valve after the tray assembly is coupled to the base unit. At 1856, a fluid pump is coupled to a pump actuator on the base unit. For example, the fluid pump can be a syringe or peristaltic pump, which can be coupled to the base unit. After the cell culture assembly is prepared, any of the methods of cell culture described herein can be performed.

[0130] As described above, in some embodiments, the automated cell culture system can include an imaging device, including a microscope, that can be moved relative to the housing of the base unit to image the contents of any cell culture vessel in the automated cell culture system. In some embodiments, the microscope can be attached to a mechanical system that can move the microscope to align with the cell culture vessel or cell counting chip. The mechanical system can be any suitable assembly for moving the imaging device, such as a two-dimensional or three-dimensional gantry mechanism or a hinged robotic arm mechanism. Figures 32-34 show an exemplary embodiment of such an optical imaging system (also referred to as a microscope imaging device). The microscope imaging device 1960 can be mounted within the housing of any base unit of the cell culture system described herein. For example, the microscope imaging device 1960 can be included within base unit 1720, base unit 2020, or any other base unit described herein. Microscopic imaging device 1960 includes imaging device 1962 that can be viewed through a window or transparent portion in the top of the base unit and through cutouts (or transparent portions) in both the tray (e.g., see transparent portion 1758 described herein) and any shaker platform (e.g., the support for the tray that contacts the agitator). Thus, microscopic imaging device 1960 can be used to collect information related to the contents of the cell culture vessel and / or cell counting chip, as described herein. For example, in some embodiments, microscopic imaging device 1960 can acquire images of the cell culture vessel and / or cell counting chip during a cell culture procedure, and the images can be used to determine, for example, the density of the contents to determine the amount of cells inside the vessel (e.g., for suspension cells), or the percentage of confluence (i.e., the coverage of the area of ​​the vessel by cells), for example, for adherent cells.

[0131] The microscope imaging device 1960 includes a gantry system 1961 that provides movement of the imaging device 1962 in multiple directions relative to a housing of a base unit (not shown in FIGS. 32-34). The gantry 1961 includes a set of rails 1963, 1964, and a cross rail 1965. The cross rail 1965 is mounted relative to the rails 1963 and 1964 in the direction of arrow B and can move back and forth relative to the rails 1963 and 1964. More specifically, a first motor 1966 can drive a belt 1968 to which the cross rail 1965 is operably coupled. The imaging device 1962 is movably mounted to the cross rail 1965 and operably coupled to a belt 1969 driven by a second motor 1967 to move the imaging device 1962 in the direction of arrow B. Imaging device 1962 can be further moved in the direction of arrow C via motor 1973 to focus imaging device 1960. Thus, during operation, imaging device 1962 can be moved in the direction of arrow A via movement of rail 1965 relative to rails 1963 and 1964, in the direction of arrow B via its movement relative to rail 1966, and in the direction of arrow C relative to the base of imaging device 1960 to be positioned at a desired location relative to the cell culture vessel and / or cell counting chip.

[0132] The light(s) or light source (not shown) can be mounted on a separate multi-axis gantry above the tray assembly of the system, allowing it to be controlled to move to the same location as the microscope in the base unit. In some embodiments, the light source can be operably coupled to the same gantry as the microscope (e.g., gantry 1961) so that the microscope 1962 and light source can move together. In some embodiments, the microscope imaging device 1960 can be controlled by any of the electronic control systems and according to any of the methods described herein. For example, in some embodiments, the microscope imaging device 1960 (and any associated light source) can be controlled to automatically image the cell culture vessel (e.g., to generate a sensor output related to the cells in the vessel). A cell sensor module of the electronic control system (e.g., electronic control system 1730) or any other electronic control system described herein can receive the sensor output and produce a signal related to the amount of cells in the vessel (e.g., cell density or percentage confluence). Based on this information, the electronic control system can then generate one or more signals (e.g., valve control signals, pump control signals, agitator signals, etc.) to cause the movement of cells from within the cell culture vessel to another vessel within the system. Also mentioned, in some embodiments, the microscope imaging device 1960 can provide input for automated cell passaging or cell harvesting operations.

[0133] 35-44 show another embodiment of cell culture system 2000 for use in cell culture procedures. Cell culture system 2000 may include the same or similar components as other embodiments described herein (including cell culture system 1700) and may have the same or similar functionality as previous embodiments described herein; therefore, some details of cell culture system 2000 are not described with respect to this embodiment.

[0134] Cell culture system 2000 (also referred to herein as a "system") includes tray assembly 2001 (see, e.g., FIGS. 35-37) and base unit 2020 (see, e.g., FIGS. 38-44). For example, as shown in FIG. 35, tray assembly 2001 includes tray 2002 with handle 2014 in which the same or similar components are arranged as described above for the previous embodiment (e.g., tray assembly 1601 or 1701). For example, tray assembly 2001 includes waste container 2006 coupled to lid 2010, reagent container 2005 coupled to lid 2009, and three lids 2008 (not shown in FIGS. 35-44) configured to couple to cell culture containers. Lids 2008, 2009, and 2010 can include liquid exchange ports (also referred to as "fluid ports") and gas exchange ports, as described above for the previous embodiments. The tray assembly 2001 also includes a multi-port valve 2007 with a master port and a plurality of selectable ports, to which the lids 2008, 2009, 2010 can be selectively coupled via lengths of tubing (not shown). For example, as described herein, the lids 2008, 2009, 2010 can be pre-assembled and coupled to the multi-port valve 2007 within an overlap. For purposes of illustration, Figures 35-44 do not show the tubing and connections between the various components and the multi-port valve 2007. The multi-port valve 2007 is coupled to the tray 2002 via a mounting portion 2016 that fits into and engages a mounting pocket 2018 of the tray 2002 in a puzzle-like manner.

[0135] Waste container 2006 and reagent container 2005 are shown horizontally coupled at holder 2004. Tray assembly 2001 also includes couplers 2003, 2003′ to which cell culture vessels can be coupled as described herein. Specifically, coupler 2003 is a bracket that extends around a first end of a cell culture vessel (not shown), and coupler 2003′ is a pair of tabs that receive a flange portion on a second end of the cell culture vessel. Coupler 2003′ also functions to hold temporary shipping support 2095 to which lid 2008 is coupled during storage, shipping, and initial setup. Couplers 2003, 2003′ hold the cell culture vessel in a predetermined, fixed position on tray 2002. Beneath where the cell culture vessel is placed is transparent portion 2058 of tray 2002 (see, e.g., FIG. 36 ). In this embodiment, a pump holder 2011 is provided that can hold a pump port (not shown), as described above for the previous embodiment. As noted above, tray assembly 2001 is pre-assembled and placed in an overwrap (not shown) to maintain sterility of tray assembly 2001 during transport and storage. Figure 37 shows tray assembly 2001 when the overwrap is removed (i.e., in a sterile environment), waste container 2006 and reagent containers 2005 are removed, and fluid pump 2013 is coupled to holder 2011. As shown in Figure 37, in this embodiment, fluid pump 2013 is a syringe.

[0136] As described above for the previous embodiment, the pre-assembled tray assembly 2001 can be removably coupled to a base unit 2020. FIGS. 38-44 show the base unit 2020. The base unit 2020 includes a housing 2023 and a pump actuator 2026 partially disposed within a recess or pocket 2025 in the housing 2023. The pump actuator 2026 (see, e.g., FIGS. 38-40 ) includes a pump holder 2019 that can lock the fluid pump 2013 in place and operably connect to the pump actuator 2026. While the pump holder 2019 is shown as a slotted member that receives a syringe flange and a movable member for securing the syringe flange in place, in other embodiments, the pump holder 2019 can be any suitable structure or mechanism for securing a pump (which can be any suitable pump) to the pump actuator. The base unit 2020 also includes a valve connector 2022 configured to matingly couple to the multiport valve 2007, and a valve actuator 2021 configured to engage the multiport pump 2007 when coupled thereto. For example, as described above, when the tray assembly 2001 is coupled to the base unit 2020, the multiport valve 2007 can be decoupled from the tray 2002 and coupled to the valve connector 2022 of the base unit 2020, such that the multiport valve 2007 is operably engaged with the valve actuator 2021, as shown in Figures 40 and 41. Figure 41 is a partially exploded view showing the components of the multiport valve 2007 prior to coupling to the valve connector 2022.

[0137] In this embodiment, support plate 2059 is coupled to housing 2023 and provides receiving portion 2024 upon which tray assembly 2001 can be placed. In this embodiment, support plate 2059 is elevated above the top surface of housing 2023. FIG. 42 is a side view showing the elevation of support plate 2059. Support plate 2059 is coupled to agitator 2028 (see FIG. 44) disposed within housing 2023. As described above, agitator 2028 can be used during cell culture procedures to agitate the contents of tray assembly 2001 and any cell culture vessels coupled thereto.

[0138] FIG. 40 shows base unit 2020 with syringe 2019 coupled to syringe holder 2019 and multi-port valve 2007 coupled to valve connector 2022. FIG. 40 also shows optional mat 2070 disposed on the top surface of support plate 2059. Mat 2070 can be, for example, a rubber mat configured to protect the surface of support plate 2059 and / or to provide damping when tray assembly 2001 is agitated by agitator 2028. Similarly, in some embodiments, the support plate (or receiving portion) of the base unit can include a damping member to damp any relative movement or contact between the support plate and the container attached thereto.

[0139] 43 and 44 are opposing side views of the base unit 2020 showing the interior of the housing 2023. FIG. 43 shows the valve actuator 2022, and FIG. 44 shows the agitator 2028 and pump actuator 2026 in the pocket 2025. An electronic control system 2030 is also shown in FIG. 44. The electronic control system 2030 can be configured the same as or similar to, and function the same as or similar to, the electronic control system 1630 described above. The electronic control system 2030 can optionally communicate with other computing devices and / or within a cloud computing environment and can include some or all of the components and functionality described above with respect to FIG. 17. Although not shown, the system 2000 can also include one or more sensors and / or lights (e.g., microscopes, imaging devices, etc.), such as the microscope imaging device 1960 described herein.

[0140] 45-51 show another embodiment of a cell culture system that can be used in cell culture procedures. Cell culture system 2100 can include some of the same or similar components as other embodiments described herein and can have the same or similar functionality as previous embodiments described herein; therefore, some details of cell culture system 2100 are not described with respect to this embodiment. In this embodiment, cell culture system 2100 does not include an agitator, but includes two multiport valves / valve actuators and two fluid pumps / fluid actuators.

[0141] Cell culture system 2100 (also referred to herein as "system") includes a tray assembly 2101 and a base unit 2120. For example, as shown in FIG. 45 , tray assembly 2101 includes a tray 2102 with two multiport valves 2107 and 2107′, and four cell culture vessels 2147 are shown disposed thereon. The vessels 2147 can be pre-assembled on tray assembly 2101 or added to tray 2102 immediately prior to a cell culture procedure. For example, in some embodiments, tray assembly 2101 is provided inside an overwrap so that vessels 2147 are pre-assembled on tray 2102. The pre-assembled vessels can be coupled or detached to lids 2108 (described below) when placed within the overwrap. In preparation for a cell culture procedure, cells and reagents are loaded into the vessels and lids 2108 are coupled to the vessels before tray assembly 2101 is coupled to base unit 2120. In some embodiments, the containers 2147 are not pre-assembled on the tray 2102 (not provided in an overlap), but rather are added to the tray in preparation for a cell culture procedure, as described above. The containers are filled with cells and reagents (e.g., cell culture medium), coupled to the lids 2108, and added to the tray assembly 2101.

[0142] The lid 2108 can be configured similarly to the lids described above for previous embodiments, including cell incubator lid 803 or lid 2408. For example, the lid 2108 can include a liquid exchange port (also referred to as a "fluid port") and a gas exchange port, which can be aseptically coupled to one of the multi-port valves 2107, 2107' with tubing (not shown), as described above for previous embodiments. For example, two of the vessels 2147 / lids 2108 can be fluidly coupled to valve 2107, and two of the vessels 2147 / lids 2108 can be fluidly coupled to valve 2107'. In this embodiment, the multi-port valves 2107, 2107' are secured to the tray 2102 and remain on the tray 2102 when the tray assembly 2101 is coupled to the base unit 2120. The multi-port valves 2107, 2107' can each include a master port and a plurality of selectable ports to which the lid 2008 (and / or other lids / containers) can be selectively connected via lengths of tubing (not shown). The multi-port valves 2107, 2107' can be connected to the tray 2102 via mounting portions (not shown) that fit into and connect to mounting pockets 2018 of the tray 2102.

[0143] In this embodiment, the base unit 2120 includes a housing 2123 that defines a tray receiving portion 2124 and that includes two valve actuators 2122, 2122′. The valve actuators 2122, 2122′ each include a valve connector portion 2171, 2171′ that extends from a top surface of the base unit 2120 within the receiving portion 2124, as shown in FIG. 51. When the tray assembly 2101 is coupled to the base unit 2120, the multiport valves 2107, 2107′ can operably engage the valve actuators 2122 and 2122′ of the base unit 2120 via the valve connector portion 2171, as shown in FIG.

[0144] In this embodiment, the base unit 2120 also includes two fluid actuators 2126 and 2126′ that can be coupled to fluid pumps 2113 and 2113′, respectively. The fluid pumps 2113 and 2113′ can be, for example, syringes, peristaltic pumps, or another type of positive displacement fluid pump. The use of the two pumps 2113 and 2113′ and two valves 2107 allows for separate fluid connections between the valves 2107 and 2107′ and various reservoirs of the system, for example, allowing separate fluid injections and evacuation from specific reservoirs (e.g., reservoir 2147). For example, waste removal from one reservoir can be separate from fresh media in another manner, avoiding passing through the same fluid channel. Two pumps can also allow for more injections and evacuation of reservoirs by duplicating the fluidics.

[0145] In this embodiment, system 2100 does not include an agitator. Although not shown, system 2100 may also include an electronic control system, one or more sensors (e.g., a microscope, an imaging device, etc.). System 2100 may also include various other containers, such as waste containers, reagent containers, cell collection containers, etc., each of which may be connectable to one of multiport valves 2107, 2107′.

[0146] 52-58 illustrate another embodiment of a cell culture system that can be used in cell culture procedures. Cell culture system 2200 can include some of the same or similar components as other embodiments described herein and can have the same or similar functionality as previous embodiments described herein; therefore, some details of cell culture system 2200 may not be shown or described in detail with respect to this embodiment. This embodiment illustrates an exemplary cell culture system that includes multiple separate tray assemblies, each of which can include lids and / or containers that can be fluidly coupled to a separate multiport valve and a separate fluid pump system. Stated differently, each tray assembly is fluidly coupled to its own multiport valve and fluid pump but is fluidly isolated from the multiport valves and fluid pumps of other trays. The individual tray assemblies can then be coupled to a single base unit. In some embodiments, each of the separate tray assemblies can be pre-assembled, placed inside a protective overwrap, and shipped separately. In some embodiments, the separate tray assemblies can be pre-assembled and shipped together within the protective overwrap. The cell culture system can culture multiple different cell types without the risk of cross-contamination by maintaining each tray assembly fluidically isolated from the other tray assemblies. For example, each tray assembly can be configured for a different cell type. This embodiment also allows for more different cell types to be cultured and incubated within a smaller device. For example, in a multi-tray system such as the one described below, the system can be used to grow three cell types on a single shelf and / or within a single base unit of an incubator without sharing fluids between the three cell types. In some embodiments, if it is desired to grow more cells of a single type, a single larger tray (two or three of the smaller trays wide) can be used.

[0147] In this embodiment, cell culture system 2200 (also referred to herein as "system") includes a base unit 2220 and three tray assemblies 2201, 2201', 2201" that can be coupled to base unit 2220 as described above for the previous embodiment. The three tray assemblies (collectively referred to as tray assemblies 2201) and base unit 2220 can include the same or similar features and components as described above for the previous embodiment. This embodiment also includes three multiport valves 2202, 2207', 2270" (collectively referred to as multiport valves 2207) and three fluid pumps 2213, 2213', 2213" (collectively referred to as fluid pumps 2213).

[0148] In this embodiment, tray assembly 2201 can each include trays 2202, 2202', 2202" (collectively referred to as trays 2202) (see, e.g., FIG. 55 ) on which are disposed multiport valves 2207, 2207', 2207", cell counting chips 2217, 2217', 2217" (collectively referred to as counting chips 2217), first cell culture vessels 2247, 2247', 2247" (collectively referred to as cell culture vessels 2247), and second cell culture vessels 2248, 2248', 2248" (collectively referred to as cell culture vessels 2248). In this exemplary embodiment, vessel 2247 is smaller than vessel 2248. However, it should be understood that tray assembly 2201 can accommodate vessels of other sizes not shown. In some embodiments, one or all of tray assemblies 2201 can include the same two vessels. The use of larger vessels (e.g., 2247) and smaller vessels (e.g., 2248) within the same tray assembly 2201 may be desirable, for example, for use in a cell expansion process. For example, cells may be placed in the smaller vessel 2248 to promote better expansion when fewer cells are present, and then the cells may be moved to the larger vessel as the growth surface of the smaller flask becomes crowded during the expansion process. The use of vessels of the same size within the same tray assembly 2201 may be desirable, for example, for a cell maintenance process to culture and maintain a cell line for the next time it is needed.

[0149] The tray 2202 can include transparent portions or partial cutouts 2258 and 2258′, as shown in FIG. 57 , in which the vessels 2247 and 2248, respectively, can be placed. As described above for the previous embodiment, the transparent portions or partial cutouts 2258, 2258′ can provide sensor data acquired related to the cell culture vessels 2247 and 2248. For example, an imaging device or other sensor can be movably disposed within the housing of the base unit 2220 (described below) and moved to a position below the transparent portions or cutouts 2258, 2258′. As shown in FIG. 57 , the transparent portion or cutout 2258′ represents an optional vessel cradle that can accommodate vessels of two different sizes. Similarly, the tray 2202 also includes a transparent portion or cutout 2268 where the cell counting chip 2217 is placed to provide sensor data acquired related to the sample fluid placed in the cell counting chip 2217, as described above for the previous embodiment.

[0150] Containers 2247 (and 2247′, 2247″) and 2248 (and 2248′, 2248″) may be pre-assembled on tray 2202 or added to tray 2202 prior to a cell culture procedure (e.g., according to methods described herein). For example, in some embodiments, container 2247 is pre-assembled on tray 2202 and tray assembly 2201 is provided within an overwrap (not shown, but similar to the overwraps described herein). The pre-assembled containers can be coupled to or detached from lid 2208 (described below) inside pre-assembled tray 2202. In preparation for a cell culture procedure, cells and reagents can be added to containers 2247, 2248 and lid 2280 attached to containers 2247, 2248 before tray assembly 2201 is coupled to base unit 2220. In some embodiments, containers 2247 are not pre-assembled (provided in an overwrap) on tray 2202, but rather are added to tray 2202 in preparation for a cell culture procedure. Containers 2247, 2248 can be filled with cells and reagents, coupled to lids, and added to tray assembly 2201.

[0151] The lid 2208 can be configured similarly to the lids described above for the previous embodiments. For example, the lid 2208 can include a liquid exchange port (also referred to as a "fluid port") and a gas exchange port. The fluid port can be aseptically coupled to one of the multi-port valves 2202, 2207', 2270" with tubing (not shown), as described above for the previous embodiments. For example, for each tray assembly 2201, the two containers 2247 and 2248 to which the lid 2208 is coupled can be fluidly coupled to select ports of the valve 2207 for that tray assembly 2201. The multi-port valves 2207 can each include a master port and multiple selectable ports to which the lid 2208 (and / or other lids / containers) can be selectively coupled. The multi-port valve 2207 can be coupled to the tray 2202 via mounting portions (not shown) that fit into and couple to mounting pockets (not shown) of the tray 2202 in a puzzle-like manner, as described above for the previous embodiments.

[0152] In this embodiment, base unit 2220 includes housing 2223 defining tray-receiving portions 2224 capable of receiving each of three tray assemblies 2201. Housing 2223 also defines section 2278, which may be a transparent portion or cutout corresponding to transparent portion 2258 of tray assembly 2201. Housing 2223 also defines section 2279, which may be a transparent portion or cutout corresponding to transparent portion 2268 of tray assembly 2201 in which cell counting chip 2217 is located. As shown in FIGS. 52-54 , base unit 2220 can also optionally include a plurality of vials or containers 2280 and a plurality of vials or containers 2249. Containers 2280 (2280′, 2280″) may be, for example, holders for associated fluid pumps 2213. For example, fluid pump 2213 may be, e.g., a peristaltic pump, and each of vessels 2280 may function as a holder for one of the pumps, such that the pumps can function similarly to a syringe-type pump. More specifically, vessel 2280′ may be a holder for fluid pump 2213′, and vessel 2280″ may be a holder for fluid pump 2213″. Retainer 2280 can receive a volume of fluid from a first location in the system where it is held until the pump is actuated to move that volume of fluid to a second location in the system. Vessels 2249 (2249′, 2249″) can be used to hold various other fluids that can be fluidly coupled to one of the separate fluid systems via one of multiport valves 2202 (2270′, 2207″). For example, vessel 2249 can be used for waste or to hold a fluid (e.g., a reagent) to warm the fluid after it has been refrigerated. For example, it may be desirable to refrigerate a container (or vessel) to maintain the medium therein at a desired temperature (e.g., 4 degrees Celsius). The medium can be pumped from refrigeration into a vessel such as vessel 2249, so that the medium can passively heat up, for example, to 37 degrees Celsius, due to the temperature of the incubator in which system 2200 is located.

[0153] When coupled to the base unit 2220, each tray assembly 2201 (2201′, 2201″) can be fluidly connected to one of the fluid pumps 2213 (2213′, 2213″) to provide a separate closed fluid flow system. As described above, when the tray assembly 2201 (2201′, 2201″) is coupled to the base unit 2220, the multiport valves 2207 (2207′, 2207″) can be operably engaged with the valve actuators 2221, 2221′, 2221″ (collectively referred to as valve actuators 2221) of the base unit 2220 via the valve connector portions 2222, 2222′ and 2222″, respectively (collectively referred to as valve connectors 2222). More specifically, in this embodiment, the multiport valves 2207 are removably coupled to the tray 2202, for example, in the case of the multiport valve 2007, they may be coupled to separate valve connectors 2222 (2222′, 2222″) (see, e.g., FIG. 54 ) and valve actuators 2221 (2221′, 2221″) of the base unit 2220 as described above. The fluid pumps 2213 may each be fluidly coupled to a master port of a corresponding multiport valve 2207. The fluid pumps 2213 (2213′, 2213″) may each be coupled to a pump actuator (not shown) that may be within or coupled to the housing 2223 of the base unit 2220. Although the fluid pumps 2213 are described as peristaltic pumps, the fluid pumps 2213 may be other types of fluid pumps, such as a syringe or another type of positive displacement fluid pump.

[0154] 53, cell culture system 2200 also includes imaging device 2260 movably disposed within housing 2223 such that it can be moved into alignment with sections 2278 and 2279. Imaging device 2260 can be, for example, a microscope mounted on a gantry system, providing movement of the imaging device in multiple directions (similar to microscope imaging device 1960 described above). Although not shown for this embodiment, cell culture system 2200 can also include an agitator, an electronic control system, and one or more additional sensor(s) (e.g., in addition to imaging device 2260), as described herein.

[0155] In some embodiments, a single imaging device (e.g., 2260) and / or a single agitator can be used to image cells on all three tray assemblies 2201. In some embodiments, separate imaging devices and / or separate agitators can be used for each tray assembly. System 2200 can also include various other containers, such as waste containers, reagent containers, cell collection containers, etc., each of which can be connected to one of the fluidic systems via multiport valves 2207, 2207′, 2207″. Cell culture system 2200 can also include various couplers or coupling portions for holding cell culture containers (e.g., 2003, 2103) and holders for holding other containers, such as waste and reagent containers (e.g., 2005, 2006).

[0156] Figure 58 shows an example of two incubators 2275 stacked on top of each other, allowing multiple cell culture systems 2200 (i.e., trays and base units) to be placed for cell culture procedures. As shown in Figure 58, in this embodiment, three cell culture systems 2200 can be placed on shelves inside each incubator 2275.

[0157] 59 is a system diagram showing exemplary fluid flows within the system during a cell culture procedure, as well as various vessels and other components that may be coupled within the cell culture systems described herein. Thus, although the system diagram is described with respect to various components of cell culture system 2300, it should be understood that this exemplary diagram is applicable to any of the embodiments described herein.

[0158] 59 shows tray 2302 coupled to two cell culture vessels 2347 and 2348. Cell culture vessels 2347 and 2348 and cell counting chip 2317 are each fluidly coupled to select ports of multiport valve 2307. A fluid pump with fluid retainer 2327 is fluidly coupled to the master port of multiport valve 2307. Multiple other vessels are also similarly fluidly coupled to multiport valve 2307, including reagent vessels 2305 and 2305′, cell collection vessel 2374, waste vessel 2360, vessel 2376 containing a cell buffer (e.g., PBS), and vessel 2377 containing an enzyme (e.g., trypsin).

[0159] During cell culture treatment, the pump holder holds the fluid solution to be pumped from a starting location in the system (e.g., reagent reservoir 2305, 2305'), valve 2307 selects the desired channel (e.g., one of reservoirs 2347, 2348), and the solution is then pumped to that location. An isotonic, non-toxic buffer solution (e.g., PBS) is used to flush reused components such as the pump holder. As shown in Supplemental Table 1 in Figure 60, in this example, reservoir 2305 can first be placed in a refrigerator to maintain the media in reservoir 2305 at a desired temperature (e.g., 4 degrees Celsius). Media from reservoir 2305 can then be pumped into reservoir 2305' prior to treatment (e.g., 1 hour before) and allowed to passively heat to approximately 37 degrees Celsius due to the incubator temperature. To dissociate cells, for example, during passaging or harvesting, medium can first be pumped out of the cell culture vessels (2347, 2348), from which the cells are dissociated and extruded for disposal. A buffer (e.g., 2376) can be added to the culture, combined with optional agitation, to wash the cells, and then the buffer can be removed from the culture, extruded, and discarded. An enzyme (e.g., in vessel 2377) can be pumped into the associated cell culture vessel, allowed to sit for a period with optional agitation to aid in dissociation, and then the solution can be diluted with fresh medium (e.g., from 2305') to quench the enzyme. The diluted enzyme in the mixture can then be used to passage / harvest / discard the cell suspension. Figures 61A and 61B include Table 2, which includes an example of a cell passaging procedure for maintaining adherent cell lines, listing each step, fluid source, destination, fluid type, and volume within each cell culture vessel during the procedure. Although specific procedures are outlined in Figure 61, system 2300 can be used to perform any of the methods for cell culture described herein (including the methods described above with reference to Figures 12-14).

[0160] 62A-62C illustrate a vessel / vessel lid 2408 according to an embodiment. The lid 2408 can be used with any of the cell culture system embodiments described herein. The lid 2408 can be threaded onto the mouth of a cell culture vessel or other vessel, as described herein, such that the lid 2408 engages with threads on the mouth of the cell culture vessel. In this exemplary embodiment, the lid 2408 has a liquid port 2483 and a gas port 2484. A liquid channel 2485 is threadably engaged with the liquid port 2483. A gas filter 2486 (see FIG. 62C) is threadably engaged with the gas port 2483. The gas filter 2486 can allow gas exchange in and out of the cell culture vessel while preventing any microorganisms or pathogens from entering the cell culture vessel. In an embodiment, the gas filter 2486 is a 0.22 micron filter.

[0161] 63A-63D show an exemplary embodiment of a multiport valve 2407, according to embodiments. The multiport valve 2407 can be used in any of the cell culture system embodiments described herein. In this embodiment, the multiport valve 2407 includes a valve body 2487 having a master port 2488 on its top surface and a plurality of selectable ports 2489 distributed around the circumference of the valve body 2487 (see, e.g., FIGS. 64A-64C).

[0162] The valve body 2487 has a cylindrical cavity on its underside into which a rotatable cylindrical valve rotor 2490 is inserted. Within the rotatable cylindrical valve rotor 2490 is a fluid channel 2491 (see FIGS. 65A-65C). Within the valve body 2487 is a fluid channel 2492 that fluidly connects a master port 2488 to the fluid channel 2491 of the valve rotor 2490. The connection between the fluid channel 2492 and the fluid channel 2491 allows the master port 2488 to be selectively fluidly connected to one of the side ports 2489 via rotation of the valve rotor 2490 (and thus the fluid channel 2491). The valve rotor 2490 includes a mechanical coupler 2493 (see FIG. 65C) configured to mechanically couple to a valve actuator of the system, which can have a cavity shaped to receive the mechanical coupler 2493 and transfer rotational mechanical energy to the multiport valve 2407.

[0163] The multiport valve 2407 can be made of any suitable material, and the valve body 2487 and valve rotor 2490 can be made of the same or different materials. Examples of materials that can be used include plastic, TFE-based materials such as polytetrafluoroethylene (PTFE), metal, rubber, or similar materials. In some embodiments, the valve body 2487 and valve rotor 2490 can be machined to fit with very close tolerances, resulting in a fluid-tight seal between the two components. In some embodiments, additional gaskets, bearings, seals, and / or flanges can be incorporated into the multiport valve 2407 to provide a fluid-tight connection between the valve body 2487 and the valve rotor 2490.

[0164] As described for some of the embodiments herein, holders and / or couplers are provided on a tray assembly, e.g., for transport purposes (e.g., for waste containers and / or reagent containers), and then the containers are removed and placed in an incubator (e.g., waste containers) or refrigerator (e.g., reagent containers). In some embodiments, the cell culture containers are provided after the overwrap is removed from the tray in preparation for a cell culture procedure. In some embodiments, the cell culture containers may be provided on the tray assembly within the overwrap (i.e., pre-assembled on the tray). For example, a sterilization method (e.g., ethylene oxide) can be used to sterilize the tray with the cell culture containers connected.

[0165] In some embodiments, rather than adding cells to a cell culture vessel in a sterile environment (e.g., a laminar flow hood), the cells can optionally be added outside the hood. For example, a lid can be provided with a sterile connector thereon, such as a septum-style connector. The lid can include a first portion (e.g., a female or male portion) of the sterile connector, and a vial of cells can include a second portion (e.g., the other of the female or male portion) of the septum connector. A vial of cells (e.g., thawed cells) can be, for example, in a flow hood. The second portion of the vial's connector can then be connected to the first portion of the sterile connection on the lid, which can be placed on a tray assembly in an incubator or at a location outside the flow hood. Thus, the vial of cells can be coupled to the tray assembly outside the sterile environment. In some embodiments, a lid with a septum can be placed on the vial of cells before the cells are frozen. In some cases, a special "freezing medium" can be added to the vial before freezing the cells to ensure that the cells are not ruptured by ice crystals during freezing. As another example, in some embodiments, cells are harvested on the system by transferring the cell suspension from the flask / vessel to a vial that has a lid with a septum connection thereon. For example, in some embodiments, the tray assembly can be shipped with a removable harvester, which can have a lid with a sterile connector as described above. After the cells are harvested, the sterile connection can then be disconnected and the vial can be removed from the tray assembly. While not shown or described in a specific embodiment above, septum-style connector lids and vessels / vessels as described above can be used in any embodiment of the cell culture system described herein.

[0166] In some embodiments, the cell culture system as described herein is capable of self-incubation. In other words, the base unit can enclose and incubate the tray. For example, the system can include a heated enclosure and appropriate gas and humidity controls. Such a system can include temperature sensors, CO and / or O sensors, humidity sensors, and an electronic control system including temperature, gas, and humidity modules for monitoring and controlling the incubator's functions.

[0167] Some portions of the preceding detailed descriptions are presented in terms of algorithms and symbolic representations of operations on data bits within a computer memory. These algorithmic descriptions and representations are the means used by those skilled in the data processing arts to most effectively convey the substance of their work to others skilled in the art. An algorithm is here, and generally, conceived to be a self-consistent sequence of operations leading to a desired result. The operations are those requiring physical manipulation of physical quantities. Usually, though not necessarily, these quantities take the form of electrical or magnetic signals capable of being stored, combined, compared, and otherwise manipulated. It has proven convenient at times, principally for reasons of common usage, to refer to these signals as bits, values, elements, symbols, characters, terms, numbers, or the like.

[0168] It should be borne in mind, however, that all of these and similar terms are associated with the appropriate physical quantities and are merely convenient labels applied to these quantities. As is evident from the above discussion, unless otherwise stated, throughout the description, discussions using terms such as "identify" or "determine" or "perform" or "do" or "collect" or "create" or "transmit" will be understood to refer to operations and processes of a computer system or similar electronic computing device that manipulate and convert data represented as physical (electronic) quantities in the computer system's registers and memory into other data that is likewise represented as physical quantities in the computer system's memory or registers or other such information storage devices.

[0169] The present disclosure also relates to apparatus for performing the operations herein. This apparatus may be specially constructed for intended purposes or may include a general-purpose computer selectively activated or reconfigured by a computer program stored in the computer. Such computer program may be stored on a computer-readable storage medium such as any type of disk, including but not limited to floppy disks, optical disks, CD-ROMs, and magneto-optical disks, read-only memory (ROM), random-access memory (RAM), EPROM, EEPROM, magnetic or optical cards, or any type of media suitable for storing electronic instructions, each coupled to a computer system bus.

[0170] Various general-purpose systems may be used with programs in accordance with the teachings herein, or it may prove convenient to construct more specialized apparatus for carrying out the methods. The structure of a variety of these systems is set forth in the description that follows. Further, this disclosure is not described with reference to any particular programming language. It will be understood that a variety of programming languages ​​can be used to implement the teachings of the disclosure, as described herein.

[0171] The present disclosure may be provided as a computer program product or software, which may include a machine-readable medium having instructions stored thereon, which can be used to program a computer system (or other electronic device) to perform a process according to the present disclosure. A machine-readable medium includes any mechanism for storing information in a form readable by a machine (e.g., a computer). For example, machine-readable (e.g., computer-readable) media includes machine (e.g., computer) readable storage media such as read-only memory ("ROM"), random access memory ("RAM"), magnetic disk storage media, optical storage media, flash memory devices, etc.

[0172] Some embodiments described herein relate to computer storage products comprising a non-transitory computer-readable medium (also referred to as a non-transitory processor-readable medium) having instructions or computer code thereon for performing various computer-implemented operations. The computer-readable medium (or processor-readable medium) is non-transitory in the sense that it does not itself comprise a transitory, propagating signal (e.g., a propagating electromagnetic wave that conveys information over a transmission medium such as space or a cable). The medium and computer code (also referred to as code) may be designed and constructed for a specific purpose. Examples of non-transitory computer-readable media include, but are not limited to: magnetic storage media such as hard disks, floppy disks, and magnetic tape; optical storage media such as compact discs / digital video discs (CDs / DVDs), compact disc read-only memory (CD-ROMs), and holographic devices; magneto-optical storage media such as optical discs; carrier wave signal processing modules; and hardware devices specially configured to store and execute program code, such as application-specific integrated circuits (ASICs), programmable logic devices (PLDs), read-only memory (ROM), and random access memory (RAM) devices.

[0173] Examples of computer code include, but are not limited to, microcode or microinstructions, machine instructions such as those produced by a compiler, code used to create a web service, and files containing high-level instructions that are executed by a computer using an interpreter. For example, embodiments may be implemented using a programming language (e.g., C, Fortran, etc.), a functional programming language (Haskell, Erlang, etc.), a logic programming language (e.g., Prolog), an object-oriented programming language (e.g., Java, C++, etc.), or other suitable programming language and / or development tools. Additional examples of computer code include, but are not limited to, control signals, encrypted code, and compressed code.

[0174] Several embodiments have been described. Nevertheless, it will be understood that various modifications can be made without departing from the spirit and scope of the present invention. Moreover, the logic flows depicted in the figures do not require the particular order shown, or sequential order, to achieve desirable results. Moreover, other steps may be provided from the described flows, or steps may be deleted, and other components may be added to or deleted from the described systems. Accordingly, other embodiments are within the scope of the following claims.

[0175] While various embodiments of the present invention have been described above, it should be understood that they are presented by way of example only, and not limitation. Where the methods above indicate that certain events occur in a particular order, the order of certain events can be changed. Additionally, certain events can be performed simultaneously in a parallel process, if possible, or sequentially, as described above. Any of the components and subcomponents described herein can be included in any of the embodiments, unless they are mutually exclusive. For example, while some embodiments may not show or describe agitators, electronic control systems, sensors, lights, various containers, etc., it should be understood that any embodiment may include one or more of these components and / or features.

[0176] As another example, while the cell culture system is described above as including a multi-port valve, in some embodiments, the cell culture system may not include the multi-port valves described herein, but instead includes one or more single-port valves. For example, in some embodiments, the cell culture assembly can include a set of single-port valves that control flow into and out of each vessel and / or lid. The set of single-port valves can be connected to a central pump by a manifold or other connection. The single-port valves can be, for example, pinch valves (which pinch the tubing connecting the vessel to another element in the system), needle valves, etc.

Claims

1. 1. An apparatus comprising: a housing defining a receiving portion; a tray assembly including a tray and a first container and a second container respectively coupled to the tray, the tray assembly configured to be received within the receiving portion of the housing; a pump actuator configured to be operably coupled to the fluid pump; a valve actuator coupled to the housing and configured to couple to a valve connectable to the first container, the valve actuator and the pump actuator collectively configured to selectively move fluid into and out of at least the first container containing a first cell sample when the tray assembly is received within the receiving portion of the housing; an electronic control system operatively coupled to the valve actuator and the pump actuator; The electronic control system includes: a cell sensor movably coupled to the housing and configured to be aligned with the first container; a cell sensor program implemented in at least one of a memory or a processor of the electronic control system and configured to generate a cell signal related to one of a density of cells and a quantity of cells in the first container based on a sensor output of the cell sensor; the electronic control system causes actuation of at least one of a valve control signal to operate the valve actuator or a pump control signal to operate the pump actuator to initiate fluid flow from the first container. Device.

2. 2. The apparatus of claim 1, wherein the electronic control system includes an actuator program implemented in at least one of a memory or a processor of the electronic control system, the actuator program configured to receive the cell signal and generate at least one of a valve control signal or a pump control signal based on the cell signal to control movement of a first volume of fluid out of the first container and into a waste container and to control movement of a second volume of fluid out of a reagent container and into the first container.

3. 10. The apparatus of claim 1, further comprising an agitator coupled to the housing and configured to engage the tray assembly when the tray assembly is coupled to the receiving portion, the agitator configured to agitate the tray assembly.

4. The device of claim 1 , wherein the cell sensor is one of an imager or a microscope coupled to the housing.

5. 2. The device of claim 1, wherein the cell sensor is an imager configured to image the first cell sample in the first container when the tray assembly is received within the receiving portion, thereby enabling at least one of confluence or density of the cells in the first container to be determined.

6. An electronic control system of a cell culture assembly receiving a sensor output from a sensor of the cell culture assembly, the cell culture assembly including a disposable tray assembly connectable to a reusable base unit, the disposable tray assembly including a tray and a first container and a second container respectively connected to the tray, the cell culture assembly including a valve actuator and a pump actuator, at least one of the first container or the second container containing a plurality of cells, and the sensor configured to be moved to align with one of the first container and the second container; generating, at the electronic control system based on the sensor output, a cell signal related to the quantity of the plurality of cells within one of the first container and the second container; and generating, based on the cell signal, at least one of a valve control signal for actuating a set of valves coupled to the valve actuators or a pump control signal for actuating a fluid pump coupled to the pump actuator to initiate fluid flow from at least one of the first container or the second container; A method comprising:

7. the set of valves includes a plurality of pinch tubes; the valve control signal causes the valve actuator to pinch at least one of the plurality of pinch tubes; The method of claim 6.

8. 1. An apparatus comprising: a housing defining a receiving portion; a tray assembly including a tray, a first container coupled to the tray, and a second container coupled to the tray, the tray assembly configured to be removably received within the receiving portion of the housing; a valve set including a first valve connected to the first container and a second valve connected to the second container; a pump actuator configured to be operably coupled to a fluid pump, the fluid pump configured to be coupled to the valve set; a valve actuator coupled to the housing and configured to be coupled to the valve set when the tray assembly is coupled to the receiving portion of the housing, the valve actuator and the pump actuator collectively configured to selectively move fluid into and out of the first container and into and out of the second container when the tray assembly is received within the receiving portion of the housing; an agitator coupled to the housing and configured to engage the tray assembly when the tray assembly is received within the receiving portion of the housing, the agitator configured to agitate the tray assembly including the first container and the second container; Device.

9. 10. The apparatus of claim 8, further comprising a sensor movably coupled to the housing and configured to generate a cell signal related to the amount of cells in the first container.

10. 10. The device of claim 9, wherein the sensor is an imager coupled to the housing and configured to image the cell sample in the first container when the tray assembly is received within the receiving portion to determine at least one of the confluence or density of cells in the first container.

11. 9. The device of claim 8, further comprising a sensor movably coupled to the housing and configured to generate a cell signal related to the amount of cells in a fluid sample in a cell counting chip coupled to the tray.

12. the first valve is a first pinch tube, and the second valve is a second pinch tube; The apparatus of claim 8 , wherein the valve actuator is configured to pinch at least one of the first pinch tube or the second pinch tube.

13. 9. The apparatus of claim 8, further comprising an electronic control system configured to control the movement of the fluid into and out of the first container and into and out of the second container when the tray assembly is received within the receiving portion.

14. when the tray assembly is received within the receiving portion, the electronic control system is configured to control movement of fluid out of reagent containers and into one of the first container or the second container through the valve set; 14. The apparatus of claim 13, wherein the electronic control system is configured to control the movement of fluid out of one of the first container or the second container and through the valve set into a waste container.

15. 9. The device of claim 8, further comprising a sensor configured to monitor a color of the cell sample in the first container when the tray assembly is received within the receiving portion, the first container including a color-based pH indicator so that a pH of the cell sample in the first container can be determined.

16. 1. An apparatus comprising: a tray assembly, the tray assembly comprising: a tray having a first transparent portion and a second transparent portion; a first container including a transparent portion, the first container being coupled to the tray such that the transparent portion of the first container is aligned with the first transparent portion of the tray; a second container including a transparent portion, the second container being coupled to the tray such that the transparent portion of the second container is aligned with the second transparent portion of the tray; a first valve connectable to the first container and a second valve connectable to the second container; the tray assembly is configured to be removably coupled to an instrument housing with the first container and the second container on the tray; Device.

17. 17. The apparatus of claim 16, wherein the first transparent portion of the tray and the second transparent portion of the tray each include one of an opening or a transparent material defined by the tray.

18. 17. The apparatus of claim 16, wherein the first valve is a pinch tube and the second valve is a second pinch tube.

19. The apparatus of any one of claims 1 to 5 and 8 to 18, wherein the tray assembly is enclosed in a wrap.

Images